. . . . . . . . . . . . . . . . . . . "2022-02-06"^^ . "The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata."@en . . "Genomic Epidemiology Ontology"@en . "GENEPIO"^^ . . "metadata section"@en . . "term as in existing standard"@en . . "term source"@en . . "The user interface label is the label that should be placed on a datum when presented on a form or report"@en . "Damion Dooley" . "user interface label"@en . . "user interface definition"@en . . "A user interface help annotation is a textual phrase to display with an entity on a form or report that provides some detail about what the entity is or how it is being used."@en . "Damion Dooley" . "user interface help"@en . "true"^^ . . "Damion Dooley" . . "user interface hidden"@en . "true"^^ . . "A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report"@en . "Damion Dooley" . "user interface feature"@en . . "This annotation can be used to select the value specification that a referenced entity or specification component has for data entry. Can be scalar value specification / categorical tree specification etc."@en . "Damion Dooley" . "obsolete: user interface value specification"@en . "true"^^ . "UI regex normalize"@en . . "Damion Dooley" . "user interface regular epression normalize"@en . "UI regex validate"@en . . "Damion Dooley" . "user interface regular expression validate"@en . "UI regex format"@en . . "Damion Dooley" . "user interface regular expression display format"@en . . . . . . . . . . . . "label" . . "see also" . . . . . . . . . . "part of"@en . . "Damion comments: In GenEpiO, If an entity has more than one value specification (in a conjunction), then it means the entitiy is a complex entity that can have a value for each specification. Minimum data requirements can be spelled out using some, min 1, max 10 etc. restrictions."@en . . "realized in"@en . . . "obsolete has string specification of"@en . "true"^^ . . . . . "T1 after t2 iff:= t2 before_or_simulataneous_with t1 and not (t1 simultaeous_with t2)"@en . "Damion Dooley"@en . "Damion Dooley's note: Intention is to have it be the inverse of \"before\". This allows axioms like \"B after A\" to be placed in class B, rather than having to phrase them as \"A before B\" in class A.\n\nI believe time dependency relations (conditions) don't imply existence by themselves. If B after A, and B exists, this doesn't necessarily mean that A exists, only that if A does exist, it must be before B. To add that extra existence implication probably requires the \"causally downstream of\" and \"immediately causally downstream of\" RO relations, in a closed system where B cannot exist any other way."@en . "after"@en . . . . "obsolete: has string value specification"@en . "true"^^ . . "obsolete: has categorical specification of"@en . "true"^^ . . . . "obsolete: has categorical value specification"@en . "true"^^ . . "has unit"@en . . . "is about"@en . "specifies"@en . . "inheres in"@en . . "has participant" . . . "location of" . . "located in" . . "aligned with"@en . . "T1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)"@en . . . . "has component"@en . . . "adjacent to" . . . "has input" . "has input"@en . . . "has output" . "has output"@en . . . . "member of" . . "has member" . "output of"@en . . . "link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch."@en . . "exactMatch"@en . . . . "An object relation between a LinkML SlotDefinition to a LocalName."@en . . . . . . "An abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated."@en . . . "Notes and comments about an element intended for external consumption."@en . . . _:genid1 . _:genid2 . _:genid3 . _:genid2 _:genid3 . _:genid4 . _:genid3 _:genid4 . _:genid4 . _:genid1 _:genid2 . _:genid1 . "Date/time at which the element was created."@en . . . "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en . "A value (string or URI) indicating the data collection state an instance of a slot has."@en . . . "A description of the element's purpose and use"@en . . . "A list of terms from different schemas or terminology systems that have identical meaning."@en . . . "Id of the schema that defined the element."@en . . . . . . "The imports entry that this element was derived from. Empty means primary source"@en . . . . . "The ncname of the source of the name."@en . . "2021-04-26T22:15:07Z"^^ . "2021-04-26T22:15:07Z"^^ . "local_name_source"@en . . . . . "A name assigned to an element in a given ontology."@en . . . . "For slots with ranges of type number, the value must be equal to or lowe than this"@en . . . . . . "For slots with ranges of type number, the value must be equal to or higher than this"@en . . . . "true means that slot can have more than one value"@en . . . . "The unique name of the element within the context of the schema. Name is combined with the default prefix to form the globally unique subject of the target class."@en . . . . "The string value of the slot must conform to this regular expression"@en . . . "A list of possible values for a slot range."@en . . . . "true if this slot is not required, but is recommended."@en . . . . "true means that the slot must be present in the loaded definition."@en . . . . "A reference."@en . . . . "IAO:0000122 ('ready for release')"@en . "status of the element."@en . . . "The uri that defines the possible values for the type definition"@en . "URI is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps)"@en . . . . . . . . "Description of what the value is doing."@en . . . . . . . "A persistent, unique identifier of a molecular sequence database entry."@en . "Damion Dooley"@en . "EDAM" . "sequence accession"@en . . . "The name of a field in a database."@en . "database field name"@en . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . _:genid5 . _:genid5 . _:genid5 . _:genid5 . _:genid6 . _:genid6 . _:genid6 . _:genid6 . _:genid7 . _:genid7 . _:genid7 "1"^^ . _:genid8 . _:genid9 . _:genid11 _:genid10 . _:genid9 _:genid11 . _:genid10 . _:genid10 . _:genid10 . _:genid11 . _:genid8 _:genid9 . _:genid7 _:genid8 . _:genid7 . _:genid12 . _:genid12 . _:genid12 "1"^^ . _:genid13 . _:genid14 . _:genid16 _:genid15 . _:genid14 _:genid16 . _:genid15 . _:genid15 . _:genid15 . _:genid16 . _:genid13 _:genid14 . _:genid12 _:genid13 . _:genid12 . . "Damion Dooley" . . _:genid17 . _:genid17 . _:genid17 . _:genid17 . . . . . . . . . . . . . . . . . . . . . . _:genid18 . _:genid18 . _:genid18 . _:genid18 . . . . . "CLSI"^^ . "NCCLS"@en . "National Committee on Clinical Laboratory Standards (NCCLS)"@en . "On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI"@en . . . . . . . . . . . . . . "depth:1"^^ . . . "order:\nARO:3004303 # nonsensitive\nARO:3004300 # intermediate\nARO:3004302 # sensitive\nARO:3004304 # sensitive - dose dependant\nARO:3004301 # resistant"^^ . "http://purl.obolibrary.org/obo/PATO_0000001"^^ . "http://purl.obolibrary.org/obo/CHEBI_50906"^^ . "Note that this can refer to a material entity like an organ or muscle, or an immaterial entity (a site or fiat boundary) like skin, stomach cavity or lung surface."@en . . . . . . . . . . . . . . . . "Trd" . . . "deoxyribonucleic acid"@en . . . "STR" . "Sm" . "Stm" . . . . . . . . . . "http://purl.obolibrary.org/obo/CHEBI_33281"^^ . "obsolete: antibiotic"@en . "true"^^ . . . . . . . . . . . "Am" . "Amk" . . . . "Amx" . . "PAS" . . . . . . "Rif" . . . . . . . . . . . . "Pto" . . . . . "CAP" . "Cm" . . . . . . . "Clr" . . "Cfz" . . . . . . "CYC" . "Cs" . . "pyrazinamide"@en . "Pza" . . . . . . . . "E" . "ETB" . "Emb" . . . . . "ETH" . "Eto" . . . . "Currently \"K antigen\" is a CHEBI_73772 chemical entity rather than a role."@en . "K antigen"@en . . . . "Inh" . "isoniazid"@en . . . . "Kan" . . "Lfx" . . . . "Lzd" . . . . "MXF" . "Mfx" . _:genid19 . _:genid19 . _:genid19 . _:genid19 "Mfx" . _:genid19 "https://www.ncbi.nlm.nih.gov/books/NBK247415/bin/part3-m17.pdf"^^ . . . . . . . . . . "Bdq" . _:genid20 . _:genid20 . _:genid20 . _:genid20 . "Damion Dooley's note: 'K antigen' can't be a subclass of antigen as chemical entity is disjoint from role."@en . "Snomed: Concept 260824002" . . . . . . . "Ofx" . . . . . . . . . . . . . . . . . . . . . . "specimen extraction matrix"@en . "\"This observable is important where process of capturing sample can affect dna extraction.\""@en . . . . . . . . . . . "http://purl.obolibrary.org/obo/OGMS_0000031"^^ . . . . . . . _:genid21 . _:genid21 . _:genid21 . _:genid21 . "state / province / territory / region"@en . "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . "Transmission of a disease agent (infectious pathogen, toxic chemical, etc.) from a source that is common to those who acquire the disease. Common vehicles include air, water, food, injected substances. Legionellosis is an example of common vehicle spread in air that has passed through air conditioning equipment contaminated by the causal organism. HIV disease and hepatitis B and C can be spread among illicit drug users by the common vehicle of contaminated needles and syringes. Cholera and many other waterborne diseases are spread by the common vehicle of contaminated water."@en . "common vehicle transmission"@en . . . . . . . . "A role that inheres in a material that is input as the subject of interest in a scientific technique - either as an entity about which data is generated in an assay or study, or an entity that is transformed or modified in a material processing technique (e.g. the source from which a biological sample is taken)" . "experimental subject role" . . . _:genid22 . _:genid22 . _:genid22 . _:genid22 . _:genid23 . _:genid23 . _:genid23 . _:genid23 . "depth:1" . . "https://en.wikipedia.org/wiki/Medical_state"@en . "condition"@en . "medical condition"@en . "medical state"@en . "Damion Dooley note: GenEpiO includes various health status descriptors here; many are annotated as included in the American AHA HIPPA or United Kingdom NHS terminologies. The challenge is to map them or order them in such a way that merged data can be analyzed."@en . "http://semanticscience.org/resource/SIO_010057"^^ . _:genid24 . _:genid24 . _:genid24 . _:genid25 . _:genid25 . _:genid25 . _:genid24 _:genid25 . _:genid24 "Condition"@en . _:genid26 . _:genid26 . _:genid26 . _:genid27 . _:genid27 . _:genid27 . _:genid26 _:genid27 . _:genid26 "Condition"@en . . . "The process of drawing in by breathing."@en . "http://purl.obolibrary.org/obo/ExO_0000057"@en . "inhalation"@en . . . "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential"@en . "MIxS"@en . . . . "A symptom onset date is a date-time entity that marks the start of one or more reported symptoms pertaining to an episode of human or animal illness"@en . "Damion Dooley" . "symptom onset date"@en . . . . "A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure."^^ . "Damion Dooley" . . "foodon product type"@en . . "lookup" . . . . "lookup" . . . . . . . . . "lookup" . . . . . . . "food packing medium"@en . . . . . . . . . . . . . . . . . . . . . . . . . "[Oceans and Seas]"@en . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . "Census Regions and Divisions are groupings of States that subdivide the United States."@en . "Damion Dooley"@en . "United States Census Bureau"@en . "http://www.census.gov/econ/census/help/geography/regions_and_divisions.html" . . . "A census region in the United States of America"@en . "Damion Dooley" . . . "A census region in the United States of America"@en . "Damion Dooley" . . . "A census region in the United States of America"@en . "Damion Dooley" . . . "A census region in the United States of America"@en . "Damion Dooley" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . "directly governed city (North Korea)"@en . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . "GSCID-BRC standard"@en . . "The GSCID-BRC Project and Sample Application Standard captures standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases."@en . "The NIAID page for specifications has a broken link for Core Project. This is the existing page:\n\nhttps://www.niaid.nih.gov/research/dmid-metadata-standards-core-project\n\nLink page is:\n\nhttps://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards"@en . "Damion Dooley" . "This standard was developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs), and NIAID and informed by discussions and input with numerous collaborating scientists."@en . "GSCID-BRC Project and Sample Application Standard"@en . . . "MIxS standard"@en . . "MixS is a unified standard for describing sequence data provided by the Genomic Standards Consortium (GSC)"@en . "Damion Dooley"@en . "Minimum Information about any (x) Sequence (MIxS)"@en . . . "MIMARKS standard"@en . "The \"minimum information about a marker gene sequence\" (MIMARKS) is a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences."@en . "http://www.nature.com/nbt/journal/v29/n5/full/nbt.1823.html"^^ . "Minimum information about a marker gene sequence"@en . . . . "\"other (metadata choice)\" indicates that for the given categorical variable, a respondent has chosen an other or additional response not listed."@en . "This class cannot be referred to directly as a subclass of more than one class without involving inference from the respective classes. Instances of it may exist as a kind of metadata. Usually a reference to a parent categorical class, but not a subordinate, carries the same information."@en . "Damion Dooley"@en . "other (metadata value)"@en . . . "other relevance"@en . . . "other"@en . . "Other: specify the sample scope that was used."@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/" . "other specimen scope"@en . . . "other material"@en . . "Other: specify the material that was used."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "other material derived from specimen"@en . . . . "\"other capture type\" is a free text description provided to indicate a target capture specification not covered by the other types."@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "other capture type"@en . . . . "Specify the project method"@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "other project method"@en . . "This is an organizational category for grouping parameters relevant to a biomedical sample."@en . "Damion Dooley"@en . . "obsolete: draft GenEpiO BioSample standard"@en . "true"^^ . . "An NCBI antibiogram data item is an antimicrobial susceptibility and resistance datum related to drug resistant pathogens. This information is provided within an antibiogram table on BioSample records."@en . "Damion Dooley" . . . "obsolete: NCBI antibiogram data item"@en . "true"^^ . . . "HIPPA PHI guideline"@en . "The American HIPPA Protected Health Information (PHI) guidelines cover information, including demographic information, which relates to:\n\n- the individual\u2019s past, present, or future physical or mental health or condition,\n- the provision of health care to the individual, or\n- the past, present, or future payment for the provision of health care to the individual, and that identifies the individual or for which there is a reasonable basis to believe can be used to identify the individual. Protected health information includes many common identifiers (e.g., name, address, birth date, Social Security Number) when they can be associated with the health information listed above.\""@en . "https://en.wikipedia.org/wiki/Health_Insurance_Portability_and_Accountability_Act"^^ . "American HIPPA Protected Health Information (PHI) guidelines"@en . . "The natural (as opposed to laboratory) full scientific taxonomic name of a subject related to a given investigation, study and/or specimen."@en . "Damion Dooley" . . "http://purl.obolibrary.org/obo/GENEPIO_0001567"^^ . "obsolete: subject species"@en . "true"^^ . . "http://purl.obolibrary.org/obo/NCIT_C45908"^^ . "NCBI BioSample: intersex"@en . "obsolete: intersex"@en . "true"^^ . . "Isolation date" . "inferred from BCCDC interviews" . "date the strain was isolated" . "Damion Dooley" . "http://purl.obolibrary.org/obo/GENEPIO_0000021"^^ . "obsolete: isolation date"@en . "true"^^ . . . "Collection" . "Culture isolation date" . "suggested in metadata feedback" . "year/month/day" . "A culture isolation date is a date-time entity marking the end of a process in which a sample is isolated as a single colony or non-mixture culture"@en . "Damion Dooley" . "GROUP: IRIDA Ontology (Morag)" . "GENEPIO" . "culture isolation date"@en . . . "Collection" . "Frozen date" . "NML Labware LIMS" . "year/month/day"@en . "A culture frozen date is a date-time entity marking the beginning of a process in which a sample culture is frozen for preservation."@en . "Damion Dooley"@en . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "culture frozen date"@en . . . "Collection" . "Received date" . "NML Labware LIMS" . "year/month/day" . "date lab received isolate" . "NML LIMS" . "GENEPIO" . "isolate received date"@en . . . "Collection" . "Upload date" . "NML Labware LIMS" . "month/day/year" . "date the isolate was entered into the database" . "NML LIMS" . "PulseNet: UploadDate" . "GENEPIO" . "isolate upload date"@en . . . _:genid28 . _:genid28 . _:genid28 . _:genid28 . "Pathogen Isolate" . "inferred from BCCDC interviews" . "gut, spine, tongue, lung"@en . "Name of body site where the specimen was obtained from, such as a specific organ or tissue."@en . "Damion Dooley's note: Although term mentions \"site\" in label, this cannot be placed under \"site\" as it is intended to refer to organism material, and leads to unsatisfiable terms otherwise."@en . "GROUP: MIxS" . "GENEPIO" . "subject anatomical site"@en . "http://gensc.org/ns/mixs/host_body_site"^^ . . . "depth:1"@en . "order:\nNCIT:C115935 # healthy\nNCIT:C25610 # pathologic\nNCIT:C28554 # deceased"@en . "diseased" . . "Health or disease status of a given subject at time of specimen collection."@en . "Currently this does not differ from the 'subject health status (GSCID-BRC)' item. It may be revised to have more options in the future."@en . "Damion Dooley"@en . "subject health status at time of specimen collection"@en . . . _:genid29 . _:genid29 . _:genid29 "1"^^ . _:genid29 . _:genid29 . _:genid30 . _:genid30 . _:genid30 "1"^^ . _:genid31 . _:genid32 . _:genid34 _:genid33 . _:genid32 _:genid34 . _:genid33 . _:genid33 . _:genid33 . _:genid34 . _:genid31 _:genid32 . _:genid30 _:genid31 . _:genid30 . "Environmental Isolate" . "sediment, chicken feces, cheese" . . "Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived." . "Damion Dooley"@en . "NCBI Biosample" . "specimen source context"@en . . . _:genid35 . _:genid35 . _:genid35 . _:genid35 . "Pathogen Isolate" . "feces, cerebral spinal fluid (CSF)" . . "Substance produced by the body, e.g. stool, mucus, where the specimen was obtained from."@en . "Damion Dooley"@en . "subject body product"@en . . . "Environmental Isolate" . "Geographic location depth" . "GROUP: MIxS" . "value (5m)" . "Please refer to the definitions of depth in the environmental packages" . "GROUP: MIxS" . "GENEPIO" . "collection depth datum"@en . . "The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO"@en . "http://purl.obolibrary.org/obo/ENVO_00010483"^^ . "obsolete: specimen source environmental material"@en . "true"^^ . . . _:genid36 . _:genid36 . _:genid36 . _:genid36 . . "A subject sex is the phenotypic sex of given subject (human or animal) related to a given investigation, study, and/or specimen."@en . "Damion Dooley"@en . "Gender is not used because it is a term referencing human social and cultural convention."@en . "subject sex specification"@en . . . "Environmental Isolate" . "Land use where sample was taken" . "Environment Canada Metadata" . "descriptive; type of human use (park, farm, urban)" . "Human use of land involving the management and modification of natural environment or wilderness into built environment." . "URI: http://en.wikipedia.org/wiki/Land_use" . "GENEPIO" . "specimen collection site land use"@en . . . _:genid37 . _:genid37 . _:genid38 . _:genid39 . _:genid40 . _:genid39 _:genid40 . _:genid40 . _:genid38 _:genid39 . _:genid37 _:genid38 . _:genid37 . _:genid41 . _:genid41 . _:genid41 . _:genid41 . "Environmental Isolate" . "Fecal Indicator Bacteria Number" . "Environment Canada Metadata" . "12,456 cfu" . "Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens."@en . "URI: http://www.who.int/water_sanitation_health/dwq/iwachap13.pdf" . "GENEPIO" . "fecal indicator bacteria count"@en . . . "Environmental Isolate" . "Conductivity" . "GROUP: MIxS" . "milliSiemens per centimeter" . "electrical conductivity of water" . "GROUP: MIxS enviro package" . "GENEPIO" . "conductivity measurement datum" . . . "Environmental Isolate" . "Dissolved oxygen" . "GROUP: MIxS" . "micromole per kilogram" . "concentration of dissolved oxygen" . "GROUP: MIxS enviro package" . "GENEPIO" . "dissolved oxygen concentration" . . . "GMI MDM standard"@en . . "The Global Microbial Identifier \"Minimum data for Matching\" (MDM) standard is a standard that defines essential contextual data fields to be included in genomic sequence repository records."@en . "Damion Dooley" . "the Global Microbial Identifier Minimum Data for Matching (MDM) Standard"@en . "http://www.globalmicrobialidentifier.org/-/media/Sites/gmi/News-and-events/2013/6th-meeting-2013-report.ashx?la=da"^^ . . . "Environmental Isolate" . "Soluble inorganic material" . "GROUP: MIxS" . "soluble organic material name;measurement value" . "concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc." . "GROUP: MIxS enviro package" . "GENEPIO" . "soluble inorganic material"@en . . . "Environmental Isolate" . "Soluble inorganic material" . "GROUP: MIxS" . "GENEPIO" . "soluble inorganic material concentration"@en . . . "Environmental Isolate" . "Nitrite" . "GROUP: MIxS" . "micromole per liter" . "concentration of nitrite" . "GROUP: MIxS enviro package" . "GENEPIO" . "nitrite concentration" . . . "Environmental Isolate" . "Nitrate" . "GROUP: MIxS" . "micromole per liter" . "concentration of nitrate" . "GROUP: MIxS enviro package" . "GENEPIO" . "nitrate concentration" . . . "Environmental Isolate" . "Total phosphorous" . "GROUP: MIxS" . "micromole per liter" . "total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus" . "GROUP: MIxS enviro package" . "GENEPIO" . "total phosphorous concentration" . . . _:genid42 . _:genid42 . _:genid43 . _:genid43 . _:genid45 _:genid44 . _:genid44 "12"^^ . _:genid45 . _:genid43 _:genid45 . _:genid42 _:genid43 . _:genid42 . "Environmental Isolate" . "Stream order" . "Environment Canada Metadata" . "value, 1-12" . "Stream order is a measure of the relative size of streams (The smallest tributaries are referred to as first-order streams, while the largest river in the world, the Amazon, is a twelfth-order waterway)." . "GROUP: Environment Canada Metadata" . "GENEPIO" . "stream order categorical measurement datum" . . . "Environmental Isolate" . "Density of bacteria in sample" . "Environment Canada Metadata" . "OD reading or cfu's or cells per millilitre" . "number of bacteria in sample" . "GROUP: Environment Canada Metadata" . "GENEPIO" . "bacteria density" . . . "Lab Analytic" . "Host Primary Enzyme" . "PulseNet Data Capture" . "pick list (XbaI, BlnI)" . "Restriction enzyme for first characterization" . "GROUP: IRIDA Ontology (Emma)" . "primary enzyme (LMAAI)"@en . . . _:genid46 . _:genid46 . _:genid46 "1"^^ . _:genid46 . _:genid46 . _:genid47 . _:genid47 . _:genid47 "1"^^ . _:genid47 . _:genid47 . . "GENEPIO" . "PFGE test specification"@en . . . "Lab Analytic" . "Host Primary PFGE Pattern" . "NML LIMS" . . "First PFGE pattern from given diagnostic restriction enzyme" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "PFGE primary test"@en . . . "Lab Analytic" . "Host Secondary Enzyme" . "PulseNet Data Capture" . "pick list (XbaI, BlnI)" . "Restriction enzyme for second characterization" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "secondary enzyme (LMACI)"@en . . . "Lab Analytic" . "Host Secondary PFGE Pattern" . "NML LIMS" . . "Second PFGE pattern from given diagnostic restriction enzyme" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "PFGE secondary test"@en . . . "Lab Analytic" . "MLST Clonal Complex" . "inferred from BCCDC interviews and Bionumerics" . "pick list?" . "Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. Sequence types are grouped into clonal complexes by their similarity to a central allelic profile (genotype). As such, clonal complexes represent sequence types that share a number of identical alleles e.g. 5/7" . "URI: http://en.wikipedia.org/wiki/Multilocus_sequence_typing ; http://eburst.mlst.net/3.asp" . "GENEPIO" . "MLST clonal complex" . . . "Lab Analytic" . "MLST Sequence Type" . "inferred from BCCDC interviews and Bionumerics" . "pick list?" . "Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. For each housekeeping gene, the different sequences present within a bacterial species are assigned as distinct alleles and, for each isolate, the alleles at each of the loci define the allelic profile or sequence type (ST)." . . "GENEPIO" . "MLST sequence typing" . . . . "The process of fingerprinting the core genome of a bacteria."@en . "Add under upcomming OBI \"DNA fingerprinting assay\"."@en . "Damion Dooley"@en . "Some bacteria like E coli have a highly variable genome, and so to type them methods must focus on typing the core genome that is common to all strains."@en . "GENEPIO" . "core genome fingerprinting assay" . . . "Lab Analytic" . "CGF type" . "inferred from BCCDC interviews" . "pick list" . . "output of CGF" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "CGF type" . . . "Lab Analytic" . "16S rRNA sequencing" . "inferred from BCCDC interviews" . "16S ribosomal RNA sequencing is a sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study."@en . "URI: http://www.illumina.com/applications/microbiology/microbial-sequencing-methods/16S-rrna-sequencing.html" . "GENEPIO" . "16S rRNA sequencing" . . . _:genid48 . _:genid48 . _:genid48 . _:genid48 . "Lab Analytic" . "Stx toxin type" . "metadata feedback" . "Stx1 or Stx2" . "pathogenic shiga toxin produced by STEC E. coli" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "Stx toxin type datum"@en . . . _:genid49 . _:genid49 . _:genid49 . _:genid49 . "Lab Analytic" . "Stx toxin subtype" . "metadata feedback" . "stx1a, stx1c" . "shiga toxin variant" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "Stx toxin subtype datum"@en . . . _:genid50 . _:genid50 . _:genid50 . _:genid50 . "Lab Analytic" . "Stx1 Toxin PCR result" . "NML Labware LIMS" . "CT value?" . "qPCR result of Stx1 gene amplification" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "Stx1 Toxin PCR result" . . . _:genid51 . _:genid51 . _:genid51 . _:genid51 . "Lab Analytic" . "Stx1 Cell Culture" . "NML Labware LIMS" . "level of Stx1 toxin derived tissue culture toxicity" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "Stx1 cell culture level" . . . _:genid52 . _:genid52 . _:genid52 . _:genid52 . "Lab Analytic" . "Stx2 Toxin PCR result" . "NML Labware LIMS" . "CT value?" . "qPCR result of Stx2 gene amplification" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "Stx2 Toxin PCR result" . . . _:genid53 . _:genid53 . _:genid53 . _:genid53 . "Lab Analytic" . "Stx2 Cell Culture" . "NML Labware LIMS" . "value?" . "level of Stx2 toxin derived tissue culture toxicity" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "Stx2 cell culture level" . . . _:genid54 . _:genid54 . _:genid54 . _:genid54 . . "An AccuProbe assay that uses a luminometer and DNA probe designed to identify a specific bacteria or fungus species within a culture."@en . "Damion Dooley"@en . "Nucleic acid hybridization tests are based on the ability of complementary nucleic acid strands to specifically align and associate to form stable double-stranded complexes (6). The ACCUPROBE method uses a single-stranded DNA probe with a chemiluminescent label that is complementary to the ribosomal RNA of the target organism. After the ribosomal RNA is released from the target organism, the labeled DNA probe combines with the target organism\u2019s ribosomal RNA to form a stable DNA:RNA hybrid. The Selection Reagent allows for the differentiation of non-hybridized and hybridized probes.The light signal emitted by the DNA:RNA hybrids is measured by a GEN-PROBE luminometer. A positive result is a luminometer reading equal to or greater than the cut-off. A value below this cut-off is the negative result."@en . "GENEPIO" . "AccuProbe culture identification assay"@en . . . . "An AccuProbe reagent kit for identifying Listeria monocytogenes."@en . "Damion Dooley"@en . "URI: http://www.hologic.com/sites/default/files/package%20inserts/103051F-EN-RevC.pdf" . "GENEPIO" . "AccuProbe Listeria monocytogenes culture identification reagent kit"@en . . . _:genid55 . _:genid55 . _:genid55 . _:genid55 . "Lab Analytic" . "NML Labware LIMS" . "positive, negative, not done" . "A categorical diagnostic result of an AccuProbe test."@en . "NML LIMS" . "GENEPIO" . "AccuProbe test result" . . . "Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. By digesting the genes with a specific restriction enzyme, fragments of different lengths are generated. By performing a Gel electrophoresis with the digested samples, the fragments can be visualised as lines on the gel, where larger fragments are close to the start of the gel, and smaller fragments further down. After blotting onto a matrix and probing, these lines form a unique pattern for each species and can be used to identify the origin of the DNA, almost like a barcode can identify a product." . . "GENEPIO" . "ribotyping" . . . "This method is based on restriction endonuclease digestion of bacterial chromosomal DNA, followed by Southern hybridization to probes for sequences in the regions of bacterial DNA coding for the 5S-16S-23S (the Escherichia coli rrnB rRNA operon) rRNA operon. The probes have been developed that are directed to highly conserved regions of the rRNA operon present in all eubacteria and can therefore be used for ribotyping most bacteria" . . "GENEPIO" . "riboprinting" . . . "an automated system that takes a purified bacterial suspension, lyses the cells, extracts the DNA, restriction endonuclease digests the DNA, separates the digest on a gel, transfers the DNA bands to a membrane, probes the bands with non-radioisotope-labeled, 5S-16S-23S rRNA-specific probes (Southern hybridization), photographs the membrane, and finally compares the bar code-like pattern to databases in order to identify the genus and species." . . "GENEPIO" . "Qualicon (DuPont) RiboPrinter Microbial Characterization System" . . . "a library of RiboPrinter recognised patterns" . "GENEPIO" . "DuPont identification pattern library" . . . "Lab Analytic" . "Riboprinter DUP Number" . "NML Labware LIMS" . "DUP-PST1-1211" . "DuPont identification number from the DuPont identification library" . "NML LIMS" . "GENEPIO" . "RiboPrinter DUP Number" . . . "Lab Analytic" . "Riboprinter DUP similarity" . "NML Labware LIMS" . "The identification of an isolate was determined when the corresponding patterns matched one of the patterns of the DuPont Identification library of the RiboPrinter1 with a similarity of >0.85. The similarity threshold for an isolate joining a ribogroup is an adaptive value between 0.90 and 0.96, depending on the size of the ribogroup." . "Similarity of pattern to one of the patterns of the DuPont Identification library of the RiboPrinter" . . "GENEPIO" . "RiboPrinter DUP similarity" . . . . _:genid56 . _:genid56 . _:genid56 . _:genid56 . "Sequencing" . "Sequencing Run Date" . "NML NGS Archive" . "yyyy/mm/dd" . "Date the sequencing run was performed"@en . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "sequencing run date"@en . . . "Sequencing" . "Sequencing Location" . "inferred from BCCDC interviews" . "location the sequencing run was performed" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "sequencing location" . . . "Sequencing" . "Platform" . "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._platform_descriptor_t/" . "Illumina (MiSeq, HiSeq), PacBio, Ion Torrent, (Roche 454), SOLiD ABI" . . "A sequencing plaform (brand) is a name of a company that produces sequencer equipment."@en . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "sequencing platform (brand)"@en . . . "Sequencing" . "Workflow" . "Derived from Sample Sheet" . "Resequencing, FastQ only" . "the workflow is the pre-defined sequence of steps to run the automated sequencing pipeline." . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "sequencing workflow" . . . "Sequencing" . "Application" . "Derived from Illumina Sample Sheet" . "amplicon sequencing, WGS" . "the sequencing application is the use or purpose of the sequencing" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "sequencing application"@en . . "Derived from Illumina Sample Sheet" . "the sequencing conditions and the analyte being measured" . "GROUP: IRIDA Ontology (Emma)" . . "obsolete: sequencing assay"@en . "true"^^ . . . "Sequencing" . "Chemistry" . "Derived from Illumina Sample Sheet" . "amplicon, resequencing (WGS)" . "lab method to determine the order of nucleotides in a DNA molecule" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "sequencing chemistry"@en . . . "Sequencing" . "Read Length" . "Derived from Illumina Sample Sheet" . "151, 251" . "number of base pairs per read" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "read length" . . "A GSCID/BRC data item is a field in one of the GSCID/BRC Project and Sample Application Standard subsets."@en . "Damion Dooley" . . "obsolete: GSCID-BRC data item"@en . "true"^^ . . . "Sequencing" . "Multiplex identifiers" . "Derived from Illumina Sample Sheet" . "S017" . "Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters" . "GROUP: MIxS" . "GENEPIO" . "sequencing run multiplex identifiers"@en . . . "Sequencing" . "Sample Name" . "Derived from Illumina Sample Sheet specification: http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/miseq/miseq-sample-sheet-quick-ref-guide-15028392-j.pdf"@en . "1,2,3, AX234, etc."@en . "Control1, Tank1, Froglet1" . "A sequencing run sample identifier is an alphanumeric identifier for a sample. In bioinformatics processing this identifier is assigned to a sample in order to track it through the process of sequencing and analysis."@en . "GROUP: IRIDA Ontology (Emma)" . "Illumina SampleSheet: Sample_ID" . "PulseNet: SubmittedNumber"@en . "sample name"@en . "sample title"@en . "GENEPIO" . "sequencing run sample identifier"@en . . . "Sequencing" . "Number of cycles" . "Derived from Illumina Sample Sheet" . "500" . "Number of sequencing chemistry cycles"@en . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "sequencing count of chemistry cycles"@en . . . "Sequencing" . "Sequencing Kit" . "Derived from Illumina Sample Sheet" . "MiSeq reagent kit" . "Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications." . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "sequencing kit"@en . . . "Sequencing" . "Sequencing Kit version" . "Derived from Illumina Sample Sheet" . "v2, v3" . "A string datum which is the version/configuration of the reagent cartidge."@en . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "sequencing kit version" . . . "Sequencing" . "Adapters" . "Derived from Illumina Sample Sheet" . "adapter A and B sequence" . "Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters" . "GROUP: MIxS" . "GENEPIO" . "adapter sequence"@en . . . "Sequencing" . "Adapter Trimming" . "Derived from Illumina Sample Sheet" . "The removal of adapter sequences from demultiplexed data reads"@en . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "read adapter trimming"@en . . . "Sequencing" . "inferred from BCCDC interviews" . "Illumina metagenomic protocol (part 15044223), with Nextera" . "Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids." . "GROUP: IRIDA Ontology (Emma) and http://applications.illumina.com/applications/sequencing/ngs-library-prep.html" . "library preparation kit" . . . "Sequencing" . "Number of base pairs" . "inferred from BCCDC interviews" . "300 000" . "The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period." . "GROUP: MIxS" . "GENEPIO" . "number of expected base pairs per genome" . . . "Run QC" . "Number of Reads Passing Filter" . "Output from MiSeq" . "0.92" . "Raw data are filtered to remove any reads that do not meet the overall quality as measured by a chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities.\nClusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6." . "URI: http://support.illumina.com/sequencing/sequencing_instruments/miseq/questions.html" . "GENEPIO" . "number of reads passing filter" . . . "Run QC" . "Cluster density" . "Output from MiSeq" . "800 k/mm^2" . "Cluster Generation is a process by which libraries amplified into clonal clusters on a flow cell. The density of those clusters in the lane, is the cluster density." . "URI: https://www.broadinstitute.org/files/shared/illuminavids/clusterGenSlides.pdf" . "sequencer flow cell cluster density" . . . "Run QC" . "above 30 Qscore" . "Output from MiSeq" . ">75%" . "percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly" . "URI: http://en.wikipedia.org/wiki/Phred_quality_score" . "GENEPIO" . "phred quality score" . . _:genid57 . _:genid58 . _:genid59 . _:genid58 _:genid59 . _:genid59 . _:genid57 _:genid58 . _:genid57 . . "Assembly QC" . "Assembly" . "Standard Term" . "the GROUP: MIxS term encompasses assembly method; estimated error rate; method of calculation" . "Assembly method refers to how the reads were assembled into contigs for which either a de novo or mapping (reference based) strategy is used." . "GROUP: MIxS" . "GENEPIO" . "assembly method" . . . "Assembly QC" . "Assembly status" . "from within \"Finishing strategy\" in GROUP: MIxS" . "standard draft or finished" . . "\"Attempting to convey the relative integrity and reliability of the data, six levels or terms have been proposed and applied to describe genome sequences.\" See subclass choices."@en . "Damion Dooley" . "CITATION: Chain, P.S., Grafham, D.V., Fulton, R.S., Fitzgerald, M.G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D.C., Buhay, C., et al. (2009). Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237." . "GENEPIO" . "assembly status"@en . . . "Assembly QC" . "Coverage" . "from within \"Finishing strategy\" in GROUP: MIxS" . "30"^^ . . "Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence." . "URI: http://en.wikipedia.org/wiki/Shotgun_sequencing" . "GENEPIO" . "Damion Dooley's note: Wikipedia defines calculation with: \"the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G\""@en . "read coverage" . . . . _:genid60 . _:genid60 . _:genid60 . _:genid60 . "Assembly QC" . "Number of Contigs" . "20"^^ . "http://purl.obolibrary.org/obo/IAO_0000428" . "A contig count is the count of contigs that belong to a sequence assembly."@en . "Damion Dooley"@en . "GENEPIO" . "contig count"@en . . . _:genid61 . _:genid61 . _:genid61 . _:genid61 . "Assembly QC" . "Assembly name" . "Standard Term" . "name and version of assemby" . "Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community" . "GROUP: MIxS" . "GENEPIO" . "assembly name (identifier)"@en . . . "Assembly QC" . "Annotation Algorithm" . "Standard Term" . "Prokka" . "Program used for annotation" . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "genome annotation algorithm" . . . "Assembly QC" . "Annotation Source" . "Standard Term" . "annotation source description" . "For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter" . "GROUP: MIxS" . "GENEPIO" . "genome annotation source" . . "Damion Dooley" . . . "obsolete: NCBI BioSample data item"@en . "true"^^ . . . "CDC ID" . . . . . "Damion Dooley" . . . "Damion Dooley"@en . . "An NCBI BioProject data item is a datum within the NCBI BioProject standard collection"@en . "Damion Dooley" . . . "obsolete: NCBI BioProject data item"@en . "true"^^ . . "The INDISC consortium \"Minimum data for Matching\" standard aims to define a format to capture reads and minimum metadata. It is developed by the \"Repository and storage of sequence and meta-data\" workgroup 2. It is used in the Global Microbial Identifier platform."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/GENEPIO_0000036"^^ . "obsolete: INSDC MDM standard"@en . "true"^^ . . "A MixS data item is a term or field defined in the Genomic Standards Consortium MIxS standard."@en . "Damion Dooley" . . "obsolete: MIxS data item"@en . "true"^^ . . . . "The 'draft data standard' class contains draft representations of formal or defacto third party standards and related components. These representations may have been crafted without any involvement of related standards issuers and so no guarantee can be provided about their currency, accuracy or veracity."@en . "Damion Dooley"@en . "draft data standard"@en . . . . "obsolete: HIPPA PHI data item"@en . "true"^^ . . . . "obsolete: PulseNet data item"@en . "true"^^ . . . . "The I2B2 Workbench Data Protection role standard is a standard which names and lists data protection roles between a user and a given dataset that define the level of detail a user has access to."@en . "Damion Dooley" . "Derived from the Data Protection Track of the I2B2 Workbench software specification: https://www.i2b2.org/software/files/PDF/current/IM_Architecture.pdf"@en . "I2B2 Data Protection role standard"@en . . . "depth:1"@en . "order:\nNCIT:C115935 # healthy\nNCIT:C25610 # pathologic / diseased\nNCIT:C28554 # deceased"@en . . "A description of whether a given subject organism appeared healthy, sick or deceased at the time of specimen extraction. If sick or deceased, additional details should be provided in project-specific fields."@en . "Damion Dooley" . "CS8" . "subject health status (GSCID-BRC)"@en . . . _:genid62 . _:genid62 . _:genid62 . _:genid62 . . "The GSCID-BRC Core Sample Standard is an extension of the GMI MDM data standard"@en . "Damion Dooley"@en . "https://www.niaid.nih.gov/research/dmid-metadata-standards-core-sample"^^ . "GSCID-BRC Core Sample standard"@en . . . . "A Core Project item is a field in the GSCID/BRC Project and Sample Application Core Project Standard."@en . "Damion Dooley"@en . "https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project" . "GSCID-BRC Core Project standard"@en . . . . "Specimen category is a categorical variable that broadly indicates the source of a specimen in order for data processing systems like NCBI's biosample submission portal to anticipate other fields related to the source. Currently this distinguishes between \"clinical or host associated\" specimens and \"environmental/food or other pathogen\" specimens."@en . "Damion Dooley" . "specimen category"@en . . . "day, week, month, year" . . "Age unit of the age measurement of a subject (individual organism)."@en . "Damion Dooley Feb 20, 2017: GSCID-BRC calls for an explicit field here whereas NCBI Biosample and MIxS don't."@en . "Damion Dooley" . "NIAID GSCID-BRC metadata working group" . "subject age - unit"@en . . . "The National Center for Biotechnology Information offers standards for submitting genomic project data to their BioProject and BioSample databases."@en . "Damion Dooley"@en . "National Center for Biotechnology Information standard"@en . "NCBI standard"@en . . . _:genid63 . _:genid63 . _:genid64 . _:genid65 . _:genid66 . _:genid65 _:genid66 . _:genid66 . _:genid64 _:genid65 . _:genid63 _:genid64 . _:genid63 . . "A datum containing the city or region or more precise geographical location identifier for the site of a specimen collection event."@en . "Damion Dooley" . "Adapted from NIAID GSCID-BRC metadata working group"@en . "Note that this is expressed in a particular format in some standards."@en . "specimen collection location - city or region"@en . _:genid67 . _:genid67 . _:genid67 . _:genid68 . _:genid68 . _:genid69 . _:genid70 . _:genid71 . _:genid70 _:genid71 . _:genid71 . _:genid69 _:genid70 . _:genid68 _:genid69 . _:genid67 _:genid68 . _:genid67 "lookup" . . . _:genid72 . _:genid72 . _:genid72 . _:genid72 . . "The country of the site of a given specimen collection event."@en . "Damion Dooley" . "NIAID GSCID-BRC metadata working group"@en . "specimen collection location - country"@en . . . . "The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries."@en . "Damion Dooley" . "http://tdwg.github.io/dwc/terms/index.htm"^^ . "Darwin Core Terms"@en . . . . "A datetime measurement related to a person's travel with respect to potential epidemilogical implications."@en . "Damion Dooley"@en . "travel history item"@en . . . . "The date of a person's departure from their primary residence (at that time) on a journey to one or more other locations."@en . "Damion Dooley"@en . "travel start date"@en . . . _:genid73 . _:genid73 . _:genid73 . _:genid73 . . "The date of a person's return to some residence from a journey originating at that residence."@en . "Damion Dooley"@en . "travel end date"@en . . . . "Infection aquired during travel is a boolean datum indicating a diagnosis of a traveller's infection during a given trip."@en . "Damion Dooley" . "infection aquired during travel"@en . . . . "This is a model of the datums involved in an epidemiology investigation."@en . "Damion Dooley"@en . "draft pathogenic epidemiology case investigation record"@en . . . . "The draft epi case exposure model describes datums related to the possible transmission of a pathogen between a case person and other people, places, animals etc."@en . "Damion Dooley" . "draft pathogenic epi case exposure record"@en . . . . "A description of a food item that a case patient has come in contact with."@en . "Damion Dooley"@en . "draft pathogenic epi case food record"@en . . . "food brought back from travel"@en . . . "An epidemiology contact network model is a definition of the information necessary to connect pathogen transmission patterns between individuals or animals in connection with an outbreak investigation."@en . "Damion Dooley"@en . "epidemiology contact network model"@en . . . . "An epi contact network - human is contact information about a person who may be involved in transmitting a pathogen."@en . "Damion Dooley" . "epi contact network model - human"@en . . . . "This is a model that provides location and transportation information about an animal that may be involved in transmitting a pathogen to a human or other animal."@en . "Damion Dooley" . "epi contact network model - animal"@en . . . "A note is text that provides human-readable information on one or more subjects."@en . "Damion Dooley" . "note"@en . . . . "An epi case general info model contains datum specifications about an epidemiology investigation case including the person involved, contact information and their demographics."@en . "Damion Dooley" . "draft pathogenic epi case general information record"@en . . . . "A record of the details around how, when, and from what an isolate was extracted."@en . "Damion Dooley" . "draft pathogenic epi case isolate detail record"@en . . _:genid74 . _:genid75 . _:genid76 . _:genid75 _:genid76 . _:genid77 . _:genid76 _:genid77 . _:genid77 . _:genid74 _:genid75 . _:genid74 . . _:genid78 . _:genid78 . _:genid78 . _:genid78 . . "A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted."@en . "Damion Dooley"@en . "specimen source substance"@en . . . . "An isolate sequence filename is the file name (http://edamontology.org/data_1050) of the contig assembly file created by a bioinformatics assembly process."@en . "Damion Dooley"@en . "isolate sequence filename"@en . . . . "A cluster identifier is an identifier that locates a genomic variant of an organism within a community of past or present genetically related organisms."@en . "Damion Dooley"@en . "cluster identifier"@en . . . . "A laboratory test performed on a specimen from a patient with regard to potential pathogenic disease."@en . "Damion Dooley" . "draft pathogenic epi case test record"@en . . . . "A lab test requestor is the individual or agency requesting that one or more tests be performed on a specimen."@en . "Damion Dooley" . "contact specification - lab test requester"@en . . . . "A food cultural origin datum indicates the cultural origin of a food product."@en . "Damion Dooley" . "food cultural origin"@en . . . . "A record of a patient's recent travel - departure and return, mode of travel and locations visited - as it may pertain to an outbreak pathogen transmission event."@en . "Damion Dooley" . "draft pathogenic epi case travel record"@en . . . "Region (England) (entry subject to GAZ replacement)"@en . . . . "An epi network contact is a person who may have recieved or transmitted an infectious disease related to an outbreak investigation."@en . "Damion Dooley" . "contact specification - epi network contact"@en . . . . "This model contains data type specifications for whole genome sequencing and epidemiology investigation contextual data."@en . "Damion Dooley" . "public health lab epidemiology contextual data standard"@en . . . "This is a set of datums involved in laboratory processing of whole-genome-sequenced isolates."@en . "Damion Dooley" . "draft whole genome sequencing lab test record"@en . . . . ""@en . "Damion Dooley" . "draft WGS lab bioinformatics process record"@en . . . . ""@en . "Damion Dooley" . "draft WGS lab sequencing record"@en . . . . "An NCBI SRA meta information item is a field specification for a NCBI Sequence Read Archive record."@en . "Damion Dooley" . "NCBI SRA meta information standard"@en . "https://www.ncbi.nlm.nih.gov/books/NBK47529/#_SRA_Quick_Sub_BK_Experiment_" . . . "An isolate raw read filename is the file name (http://edamontology.org/data_1050) of the raw read file created by a genomic sequencing assay."@en . "isolate raw read filename"@en . . . "Sequencing" . . "The version identifier of a packaged kit tailored for specific sequencing workflows."@en . "Damion Dooley"@en . "library preparation kit version"@en . . . . "The name and version of software used in a bioinformatics workflow to improve the quality of sequencing reads."@en . "Damion Dooley"@en . "read trimming and filtering software"@en . . . . ""@en . "Damion Dooley" . "bioinformatics pipeline name"@en . . . . ""@en . "Damion Dooley" . "bioinformatics pipeline version"@en . . . . ""@en . "Damion Dooley" . "bioinformatics pipeline protocol"@en . . . . ""@en . "Damion Dooley" . "draft WGS lab sequencing quality metrics record"@en . . . . ""@en . "Damion Dooley" . "draft WGS lab assembly quality metrics record"@en . . . . "A general label indicating the primary study goal. These are only relevant for Primary submission projects (not Umbrella projects)."@en . "Damion Dooley" . "Damion Dooley's note: According to http://trace.ddbj.nig.ac.jp/news/2014-11-12_e.html, \"A BioProject record can have multiple project data types\""@en . "project data type"@en . . . . "Genome assembly project utilizing already existing sequence data including data that was submitted by a different group"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "assembly project"@en . . . . "A sequencing project involving clone-ends"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "clone ends project"@en . . . . "A sequencing project involving DNA methylation, histone modification, and/or chromatin accessibility datasets"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "epigenomics project"@en . . . . "Exome resequencing project"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "exome resequencing project"@en . . . . "A whole, or partial, genome sequencing project (with or without a genome assembly)"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "genome sequencing project"@en . . . "The Relational Sequencing TB Data Platform (ReSeqTB) catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of Mtb."@en . "Damion Dooley" . "https://platform.reseqtb.org/"^^ . "draft ReSeq Tuberculosis data platform standard"@en . . . "In expressions like: \"<= 8mg/L\""@en . . "The measurement comparator is a sign indicating that a measurement is above, equal to, or below a given threshold."@en . "Damion Dooley"@en . "test threshold measurement comparator"@en . . . "<" . . "The \"less than\" comparator indicates that a given substance was present at less than a given quantity or concentration."@en . "Damion Dooley" . "<" . "less than"@en . . . "<="@en . . "The \"less than or equal to\" comparator indicates that a given substance was present at less than or equal to a given quantity or concentration."@en . "Damion Dooley" . "<=" . "less than or equal to"@en . . . "=="@en . . "The \"equal to\" comparator indicates that a given substance was present at the given quantity or concentration."@en . "Damion Dooley" . "==" . "equal to"@en . . . ">="@en . . "The \"greater than or equal to\" comparator indicates that a given substance was present at greater than or equal to a given quantity or concentration."@en . "Damion Dooley" . ">=" . "greater than or equal to"@en . . . ">"@en . . "The \"greater than\" comparator indicates that a given substance was present at greater than a given quantity or concentration."@en . "Damion Dooley" . ">" . "greater than"@en . . . "order:\nOBI:0001616 # specimen identifier\nOBI:0001614 # GenBank ID\nGENEPIO:0001100 # antibiogram drug test model\nGENEPIO:0002062 # amr testing reference standard\nGENEPIO:0002045 # amr resistance testing method\nGENEPIO:0002047 # ... version or reagent\nGENEPIO:0002049 # amr testing platform\nGENEPIO:0002056 # ... vendor" . . "The NCBI antibiogram standard details the reporting specifications for antimicrobial susceptibility and resistance data derived from drug resistant pathogens. This information is submitted as an antibiogram table on BioSample records."@en . "Damion Dooley" . "NCBI Antibiogram standard"@en . "https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/"^^ . . "http://purl.obolibrary.org/obo/GENEPIO_0001007" . "obsolete: NCBI isolate AMR testing model"@en . "true"^^ . . "A restaurant or an eatery, is a business which prepares and serves food and drinks to customers in exchange for money."@en . "Damion Dooley" . "https://en.wikipedia.org/wiki/Restaurant" . "http://purl.obolibrary.org/obo/ENVO_01000934"^^ . "obsolete: restaurant"@en . "true"^^ . . . "iPHIS standard"@en . . "The Canadian Integrated Public Health Information System (iPHIS) System provides a standard for holding reportable disease cases from participating jurisdictions."@en . "Damion Dooley" . "Canadian Integrated Public Health Information System (iPHIS) Standard"@en . . . "254532233433235152213423"^^ . . "The MIRU24 - international standard is a mycobacterial interspersed repetitive units (MIRU) typing method that classifies Mycobacterium tuberculosis complex (MBTC) bacteria according to a multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) typing scheme of counts of repeats at 24 sequence loci."@en . "The ordering of loci is as follows: MIRU 04, MIRU 26, MIRU 40, MIRU 10, MIRU 16, MIRU 31, 424\t577, 2165, 401, 3690, 4156, 2163, 1955, 4052, MIRU 02, MIRU 23, MIRU 39, MIRU 20, MIRU 24, MIRU 27, 2347, 2461, 3171"@en . "MIRU24 - international standard"@en . . . . "The MIRU24 - Canadian standard is a Mycobacterium tuberculosis typing method exactly like MIRU24 - international standard except that the report of the ordering of the matching loci is different."@en . "Damion Dooley"@en . "The ordering of loci is as follows: MIRU 02, MIRU 04, MIRU 10, MIRU 16, MIRU 20, MIRU 23, MIRU 24, MIRU 26, MIRU 27, MIRU 31, MIRU 39, MIRU 40, 424, 577, 1955, 2163, 2165, 2347, 2401, 2461, 3171, 3690, 4052, 4156"@en . "MIRU24 - Canadian standard"@en . . . "spray-wading water"@en . . . "pool water"@en . . . "obsolete: hot tub"@en . "true"^^ . . "A cafeteria is a type of food service location in which there is little or no waiting staff table service, whether a restaurant or within an institution such as a large office building or school."@en . "Damion Dooley" . "https://en.wikipedia.org/wiki/Cafeteria" . "http://purl.obolibrary.org/obo/ENVO_01000969"^^ . "obsolete: cafeteria"@en . "true"^^ . . "http://purl.obolibrary.org/obo/ENVO_00003864"^^ . "obsolete: bakery"@en . "true"^^ . . "A delicatessen or deli is a retail establishment that sells a selection of unusual or foreign prepared foods."@en . "Damion Dooley" . "https://en.wikipedia.org/wiki/Delicatessen" . "http://purl.obolibrary.org/obo/ENVO_01000970"^^ . "obsolete: delicatessen"@en . "true"^^ . . "A food kiosk is a kiosk (a booth with an open window on one side) that sells food."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/ENVO_01000974"^^ . "obsolete: food kiosk"@en . "true"^^ . . "A grocery store is a retail store that primarily sells food."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/ENVO_01000984"^^ . "obsolete: grocery store"@en . "true"^^ . . "A specialty/ethnic food store is a store specializing in a particular variety of food or food of cultural / regional origin."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/ENVO_01000988"^^ . "obsolete: specialty/ethnic store"@en . "true"^^ . . "A market, or marketplace, is a location where people regularly gather for the purchase and sale of provisions, livestock, and other goods"@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/ENVO_01000987"^^ . "obsolete: market"@en . "true"^^ . . . . "A time measurement datum that pertains to a patient's medical treatment."@en . "Damion Dooley" . "treatment history datum"@en . . "A restaurant providing prepared meals or other food items that the purchaser intends to eat elsewhere"@en . "Damion Dooley" . "https://en.wikipedia.org/wiki/Take-out"@en . "http://purl.obolibrary.org/obo/ENVO_01000972"^^ . "obsolete: take out restaurant"@en . "true"^^ . . . . "A treatment start date is a date/time datum which indicates the start of a particular medical treatment for a patient."@en . "Damion Dooley" . "treatment start date"@en . . . "canoeing / kayaking / boating"@en . . . "hiking"@en . . . "camping"@en . . "Damion Dooley" . "http://purl.obolibrary.org/obo/PCO_0000033"^^ . "obsolete: social gathering"@en . "true"^^ . . "http://purl.obolibrary.org/obo/PCO_0000035"^^ . "obsolete: party"@en . "true"^^ . . "http://purl.obolibrary.org/obo/PCO_0000038"^^ . "obsolete: wedding"@en . "true"^^ . . "http://purl.obolibrary.org/obo/PCO_0000039"^^ . "obsolete: baby shower"@en . "true"^^ . . "http://purl.obolibrary.org/obo/PCO_0000037"^^ . "obsolete: potluck"@en . "true"^^ . . "http://purl.obolibrary.org/obo/PCO_0000034"^^ . "obsolete: community event"@en . "true"^^ . . "A long term care facility provides a type of residential care. It is a place of residence for people who require continual nursing care and have significant difficulty coping with the required activities of daily living."@en . "Damion Dooley" . "https://en.wikipedia.org/wiki/Nursing_home_care" . "http://purl.obolibrary.org/obo/ENVO_01000932"^^ . "obsolete: long term care facility"@en . "true"^^ . . . _:genid79 . _:genid79 . _:genid79 . _:genid79 . . "A treatment end date is a date/time datum which indicates the end of a particular medical treatment for a patient."@en . "Damion Dooley" . "treatment end date"@en . . . "Damion Dooley" . "food related exposure event"@en . . . . "Some bacteria are associated with particular foods. Need relationship"@en . "Damion Dooley"@en . "infection-specific food detail"@en . . . . "A tuberculosis treatment antibiotic is an antibiotic used in the treatment of tuberculosis."@en . "Damion Dooley" . "tuberculosis treatment drug"@en . "\u201CTreatment of Tuberculosis Guidelines\u201D, WHO, Geneva, 2010, 30 www.who.int/tb/ - See more at: http://www.tbfacts.org/tb-drugs/#sthash.nibuzCLV.dpuf" . . . "vegetarian"@en . . . . "A time measurement datum that pertains to an organism's physical location."@en . "Damion Dooley" . "organism location history datum"@en . . . "This will take on a sub-herarchy of food types."@en . "food avoidance"@en . . . "special diet"@en . . . "water related exposure event"@en . . . "municipal water"@en . . . . "A time measurement datum indicating the year a person immigrated to a given country."@en . "Damion Dooley" . "immigration year of arrival"@en . . . "bottled water"@en . . . "An event (occuring at some location and for some duration of time) where"@en . "Damion Dooley" . "infectious disease exposure event"@en . . . "Damion Dooley" . "human related exposure event"@en . . . "Damion Dooley" . "animal related exposure event"@en . . . . "Identification or description of the specific individual from which this sample was obtained"@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/"^^ . "NCBI BioSample isolate (human name or description)"@en . . "Damion Dooley" . "http://purl.obolibrary.org/obo/ENVO_01000923"^^ . "obsolete: petting zoo"@en . "true"^^ . . . "Damion Dooley" . "agricultural fair"@en . . . "An isolate passage history is a record of the cyclic growth process that led to it, including number of times its was put through the process, and the method used."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/GENEPIO_0001835"^^ . "isolate passage history datum"@en . . . "For Eschericia coli: STEC, UPEC"@en . "A pathotype is a common name for a group of organisms (of the same species) that have the same pathogenicity on a specified host"@en . "https://en.wiktionary.org/wiki/pathotype"@en . "NCBI pathotype"@en . . . "Damion Dooley" . . "pet treat"@en . . . "Damion Dooley" . . "pet food (raw)"@en . . . . "An epidemiology travel datum is a datum regarding a particular human's travel trip destination, mode, and motivation, with respect to an epidemiology investigation."@en . "Damion Dooley" . "human exposure event - travel datum"@en . . . "boat / cruise travel"@en . . . "train travel"@en . . . "bus travel"@en . . . "car travel"@en . . . "airline travel"@en . . . . "A travel mode is a type of transportation which a given human has used while travelling on a particular trip."@en . "Damion Dooley" . "travel mode"@en . . . . "A travel reason is a motivation for traveling on a particular trip expressed by the traveller."@en . "Damion Dooley" . "travel reason"@en . . . "travel for pleasure"@en . . . "business activity"@en . . . "religious missionairy activity"@en . . . "rural backpacking activity"@en . . . "visiting relative/friends"@en . . . "travel tour"@en . . . "unsure of travel reason"@en . . . "The tuberculosis draft standard is a GenEpiO set of draft genomic and clinical data items related to Mycobacterium tuberculosis that various agencies are using in their own reporting."@en . "draft tuberculosis - specimen contextual data standard"@en . . . . ""@en . "Damion Dooley" . "" . "behavioural risk factor"@en . . "http://purl.obolibrary.org/obo/GENEPIO_0001686"^^ . "obsolete: E. coli serotype part"@en . "true"^^ . . . "Snomed: Concept 260827009" . "O antigen"@en . . . "Snomed: Concept 260823008" . "H antigen"@en . . . . ""@en . "Damion Dooley" . "" . "homeless status"@en . . . . "A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the sub-species level"@en . "Damion Dooley"@en . "https://en.wikipedia.org/wiki/Serotype"^^ . "serovar/serotype common name"@en . . . _:genid80 . _:genid80 . _:genid80 . _:genid80 . "Salmonella serovar"@en . . . "Salmonella serovar name"@en . . . _:genid81 . _:genid81 . _:genid81 . _:genid81 . "Salmonella antigenic formula"@en . . . . ""@en . "Damion Dooley" . "" . "drug use status"@en . . . . ""@en . "Damion Dooley" . "" . "incarceration status"@en . . . . ""@en . "Damion Dooley" . "" . "HIV status"@en . . . . ""@en . "Damion Dooley" . "" . "HIV risk status"@en . . . . ""@en . "Damion Dooley" . "" . "A.I.D.S status"@en . . . . ""@en . "Damion Dooley" . "" . "drug abuse status"@en . . . . ""@en . "Damion Dooley" . "" . "injection drug use status"@en . . . . ""@en . "Damion Dooley" . "" . "recreational drug use status"@en . . . . ""@en . "Damion Dooley" . "" . "methadone use status"@en . . . . ""@en . "Damion Dooley" . "" . "substantial alcohol use/abuse status"@en . . . . "" . "Damion Dooley" . "smoking status"@en . . . _:genid82 . _:genid82 . _:genid82 . _:genid82 . _:genid83 . _:genid83 . _:genid83 . _:genid83 . . "A country of birth is the country that a given person (or animal) was born in."@en . "Damion Dooley"@en . "country of birth"@en . . . "Tb_1 (with respect to an Illumina SampleSheet.csv spreadsheet)\n13 (with respect to a ReSeqTB SNP pipeline sample report)"@en . . "A sequence number is a numeric identifier of a sequence with respect to a particular data table or dataset."@en . "sequence number"@en . . . . "Damion Dooley" . "The 'date last seen alive' is the date that a subject (patient) was last known (seen, heard, messaged) to be alive."@en . "date last seen alive"@en . . . "second line or reserve tuberculosis drug"@en . . . "tuberculosis infection anatomical site"@en . . "http://purl.obolibrary.org/obo/GENEPIO_0001007" . "obsolete: NCBI Antibiogram model"@en . "true"^^ . . . "order:\nGENEPIO:0001187 # antimicrobial resistance test drug\nGENEPIO:0002112 # drug MIC\nGENEPIO:0002080 # drug minimum inhibitory concentration unit\nGENEPIO:0001001 # measurement comparator\nNCIT:C85539 # antimicrobial resistance phenotype\nGENEPIO:0002181 # antimicrobial resistance phenotype - ECOFF" . . "This is the minimal set of parameters for drug test results for a particular antimicrobial agent."@en . "Damion Dooley"@en . "draft antibiogram drug test model"@en . "http://the-vet.net/DVMWiz/Vetlibrary/Lab-%20Microbiology%20Guide%20to%20Interpreting%20MIC.htm" . "https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/"^^ . . . "A date-time datum that marks the predicted start of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time."@en . "Damion Dooley" . "predicted exposure start"@en . . . "A date-time datum that marks the predicted end of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time."@en . "Damion Dooley" . "predicted exposure end"@en . . . . "Map: - project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "map project"@en . . . . "Metagenome: sequence analysis of environmental samples"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "metagenome project"@en . . . . "Metagenome assembly: a genome assembly generated from sequenced environmental samples"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "metagenome assembly project"@en . . . . "Other: a free text description is provided to indicate Other data type"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "other project data type"@en . . . . "Phenotype or Genotype: project correlating phenotype and genotype"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "phenotype or genotype project"@en . . . . "Proteome: large scale proteomics experiment including mass spec. analysis"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "proteome project"@en . . . . "Random Survey: sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "random survey project"@en . . . . "Targeted locus (loci): project to sequence specific loci, such as a 16S rRNA sequencing"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "targeted locus (loci) project"@en . . . . "Transcriptome or Gene expression: large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "transcriptome or gene expression"@en . . . . "A sequencing project with a primary goal of identifying large or small sequence variation across populations."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "variation project"@en . . . . _:genid84 . _:genid84 . _:genid84 . _:genid84 . _:genid85 . _:genid85 . _:genid86 . _:genid86 . _:genid88 _:genid87 . _:genid87 "(Afghanistan|Albania|Algeria|American Samoa|Andorra|Angola|Anguilla|Antarctica|Antigua and Barbuda|Arctic Ocean|Argentina|Armenia|Aruba|Ashmore and Cartier Islands|Atlantic Ocean|Australia|Austria|Azerbaijan|Bahamas|Bahrain|Baltic Sea|Baker Island|Bangladesh|Barbados|Bassas da India|Belarus|Belgium|Belize|Benin|Bermuda|Bhutan|Bolivia|Borneo|Bosnia and Herzegovina|Botswana|Bouvet Island|Brazil|British Virgin Islands|Brunei|Bulgaria|Burkina Faso|Burundi|Cambodia|Cameroon|Canada|Cape Verde|Cayman Islands|Central African Republic|Chad|Chile|China|Christmas Island|Clipperton Island|Cocos Islands|Colombia|Comoros|Cook Islands|Coral Sea Islands|Costa Rica|Cote d'Ivoire|Croatia|Cuba|Curacao|Cyprus|Czech Republic|Democratic Republic of the Congo|Denmark|Djibouti|Dominica|Dominican Republic|East Timor|Ecuador|Egypt|El Salvador|Equatorial Guinea|Eritrea|Estonia|Ethiopia|Europa Island|Falkland Islands (Islas Malvinas)|Faroe Islands|Fiji|Finland|France|French Guiana|French Polynesia|French Southern and Antarctic Lands|Gabon|Gambia|Gaza Strip|Georgia|Germany|Ghana|Gibraltar|Glorioso Islands|Greece|Greenland|Grenada|Guadeloupe|Guam|Guatemala|Guernsey|Guinea|Guinea-Bissau|Guyana|Haiti|Heard Island and McDonald Islands|Honduras|Hong Kong|Howland Island|Hungary|Iceland|India|Indian Ocean|Indonesia|Iran|Iraq|Ireland|Isle of Man|Israel|Italy|Jamaica|Jan Mayen|Japan|Jarvis Island|Jersey|Johnston Atoll|Jordan|Juan de Nova Island|Kazakhstan|Kenya|Kerguelen Archipelago|Kingman Reef|Kiribati|Kosovo|Kuwait|Kyrgyzstan|Laos|Latvia|Lebanon|Lesotho|Liberia|Libya|Liechtenstein|Line Islands|Lithuania|Luxembourg|Macau|Macedonia|Madagascar|Malawi|Malaysia|Maldives|Mali|Malta|Marshall Islands|Martinique|Mauritania|Mauritius|Mayotte|Mediterranean Sea|Mexico|Micronesia|Midway Islands|Moldova|Monaco|Mongolia|Montenegro|Montserrat|Morocco|Mozambique|Myanmar|Namibia|Nauru|Navassa Island|Nepal|Netherlands|New Caledonia|New Zealand|Nicaragua|Niger|Nigeria|Niue|Norfolk Island|North Korea|North Sea|Northern Mariana Islands|Norway|Oman|Pacific Ocean|Pakistan|Palau|Palmyra Atoll|Panama|Papua New Guinea|Paracel Islands|Paraguay|Peru|Philippines|Pitcairn Islands|Poland|Portugal|Puerto Rico|Qatar|Republic of the Congo|Reunion|Romania|Ross Sea|Russia|Rwanda|Saint Helena|Saint Kitts and Nevis|Saint Lucia|Saint Pierre and Miquelon|Saint Vincent and the Grenadines|Samoa|San Marino|Sao Tome and Principe|Saudi Arabia|Senegal|Serbia|Seychelles|Sierra Leone|Singapore|Sint Maarten|Slovakia|Slovenia|Solomon Islands|Somalia|South Africa|South Georgia and the South Sandwich Islands|South Korea|South Sudan|Southern Ocean|Spain|Spratly Islands|Sri Lanka|State of Palestine|Sudan|Suriname|Svalbard|Swaziland|Sweden|Switzerland|Syria|Taiwan|Tajikistan|Tanzania|Tasman Sea|Thailand|Togo|Tokelau|Tonga|Trinidad and Tobago|Tromelin Island|Tunisia|Turkey|Turkmenistan|Turks and Caicos Islands|Tuvalu|USA|Uganda|Ukraine|United Arab Emirates|United Kingdom|Uruguay|Uzbekistan|Vanuatu|Venezuela|Viet Nam|Virgin Islands|Wake Island|Wallis and Futuna|West Bank|Western Sahara|Yemen|Zambia|Zimbabwe|Historical Country Names|Belgian Congo|British Guiana|Burma|Czechoslovakia|Former Yugoslav Republic of Macedonia|Korea|Netherlands Antilles|Serbia and Montenegro|Siam|USSR|Yugoslavia|Zaire)(:[a-zA-Z0-9 ]+)?" . _:genid88 . _:genid86 _:genid88 . _:genid85 _:genid86 . _:genid85 . "help: Consult the http://www.insdc.org/country.html country list for valid options."@en . "The INSDC country qualifier is a textual controlled vocabulary used to indicate the country of origin of a DNA sample. It can also have the following format: country:sub_region, such as: \"Canada:Vancouver\"."@en . "Damion Dooley"@en . "INSDC country qualifier"@en . . . "phenotype"@en . . "Phenotype: phenotypic measurements for submission to dbGaP"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "phenotype project objective"@en . . . _:genid89 . _:genid89 . _:genid89 . _:genid89 . "genome material"@en . . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "genome material from specimen"@en . . . "TB lineage 7 - Ethiopia"@en . . . _:genid90 . _:genid92 _:genid91 . _:genid91 . _:genid91 . _:genid93 . _:genid93 . _:genid93 . _:genid91 _:genid93 . _:genid95 _:genid94 . _:genid92 _:genid95 . _:genid94 . _:genid94 . _:genid96 . _:genid96 . _:genid96 . _:genid94 _:genid96 . _:genid95 . _:genid90 _:genid92 . _:genid90 . . "An object aggregate which has as members whole organs or parts of organs, possibly from different organisms."@en . . "2021-04-19T23:36:25Z"^^ . "organs or organ parts"@en . . . "A travel destination which a given human has travelled to on a particular trip and is outside Canada."@en . . "2021-05-27T04:35:17Z"^^ . "travel outside Canada"@en . . . "A travel destination which a given human has travelled to on a particular trip and is outside a given province/territory of interest."@en . . "2021-05-27T04:36:13Z"^^ . "travel outside province/territory"@en . . . "requires discussion"@en . "A data specification established for use by The Canadian COVID-19 Genomics Network (CanCOGeN) project DataHarmonizer application, for contextual data (metadata) harmonization and curation across data providers."@en . "https://orcid.org/0000-0002-9578-0788" . "https://github.com/Public-Health-Bioinformatics/DataHarmonizer/blob/master/template/canada_covid19/SOP.pdf" . "2021-04-24T00:18:57Z"^^ . "draft CanCOGeN DataHarmonizer specification"@en . . . . "A livespan history item is a date-associated event pertaining to the life of a subject."@en . "Damion Dooley"@en . "lifespan history item"@en . . . "untreated water"@en . . . "treated water - ambient temperature"@en . . . "epidemiology investigation data item"@en . . "Unclear semantics and origin"@en . "obsolete distribution event"@en . "true"^^ . . "obsolete supply point / event"@en . "true"^^ . . . . "well water - treated"@en . . . . "Well water - untreated" . . . _:genid97 . _:genid97 . _:genid97 . _:genid97 . "organism datum"@en . . . . . . . . . . "http://purl.obolibrary.org/obo/GENEPIO_0001171"^^ . "http://purl.obolibrary.org/obo/OBI_0100026"^^ . "http://purl.obolibrary.org/obo/PATO_0000047"^^ . . . _:genid98 . _:genid98 . _:genid98 . _:genid98 . "a role which inheres in an organism and is realized by the process of being alive" . "organism role"@en . . . "isolate organism role"@en . . _:genid99 . _:genid100 . _:genid102 _:genid101 . _:genid100 _:genid102 . _:genid101 . _:genid101 . _:genid101 . _:genid102 . _:genid99 _:genid100 . _:genid99 . . "animal role"@en . . _:genid103 . _:genid104 . _:genid106 _:genid105 . _:genid104 _:genid106 . _:genid105 . _:genid105 . _:genid105 . _:genid106 . _:genid103 _:genid104 . _:genid103 . . "plant role" . . . . "Damion Dooley" . "taxonomic datum"@en . . . . "A course of treatment designed to resolve an infectious disease"@en . "Damion Dooley"@en . "infectious disease treatment"@en . . _:genid107 . _:genid108 . _:genid110 _:genid109 . _:genid108 _:genid110 . _:genid109 . _:genid109 . _:genid109 . _:genid110 . _:genid107 _:genid108 . _:genid107 . . . "This is a collection of drugs used to test antimicrobial resistance."@en . "This is a class of chemicals by use. They are organized more indirectly in CHEBI via 'has role' some 'antimicrobial agent'.\n\nNote: NCBI provides special requirements for antibiotic test-selection for BETA-LACTAMASE, see https://www.ncbi.nlm.nih.gov/biosample/docs/beta-lactamase/\n\nDamion Dooley note: Used http://cts.fiehnlab.ucdavis.edu/conversion/batchConvert to convert antibiotic name to CHEBI entries. 60% match, some matches off, had to curate hits manually.\n\nNote that this is a longer list of antibiotics that we will need to incorporate, perhaps through ARO:\nhttps://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/?format=txt"@en . "Damion Dooley"@en . "antimicrobial resistance test drug"@en . . . . "Damion Dooley" . "Judgements here are marked down after an agent's (doctor/veterenary) analysis of symptoms."@en . "analytic datum"@en . . "Damion Dooley" . "http://purl.obolibrary.org/obo/DOID_4"^^ . "obsolete: type of illness"@en . "true"^^ . . . . "A specimen which has been confirmed by laboratory test(s) to contain a disease-causing agent such as a pathogen"@en . "Damion Dooley"@en . "specimen with confirmed presence of disease agent"@en . . . "dietary restriction"@en . . . . "A person which has a patient care role."@en . "Damion Dooley" . "patient type"@en . . . "obsolete: mother"@en . "true"^^ . . . "NCBI BioSample" . "depth:1" . "lookup" . . "A subject disease outcome is an assessment of the persistence of a given disease course in a subject (patient)"@en . "Damion Dooley"@en . "Note that this is closely related to OGMS_0000063 \"disease course\" that lists chronic, progressive, transient and accute processes."@en . "subject disease outcome"@en . . . "treated water - warm/hot"@en . . . "jacuzzi water"@en . . . "spa water" . . . "whirlpool water"@en . . . _:genid111 . _:genid111 . _:genid111 . _:genid111 . . "A host datum is a datum that pertains to infection-related information about an organism (animal or human) who is likely bearing a pathogen"@en . "Damion Dooley"@en . "patient as host datum"@en . . . "pregnancy history item"@en . . . "date of conception"@en . . . . "Damion Dooley" . "lifespan history record"@en . . "http://purl.obolibrary.org/obo/FOODON_03450002"^^ . "obsolete: food cooking method"@en . "true"^^ . . "http://purl.obolibrary.org/obo/FOODON_03470107"^^ . "obsolete: food preservation method"@en . "true"^^ . . . "infectious disease case datum"@en . . . "laboratory data"@en . . . . "Damion Dooley" . "specimen record"@en . . . . "The type of material from which the specimen was obtained. Specimens are usually categorized as food, body products or tissues, or environmental material."@en . "Damion Dooley"@en . "specimen type (host or environmental context)"@en . "specimen source material category"@en . . . "Organism has a symbiotic relationship with host"@en . "symbiotic role"@en . . "http://purl.obolibrary.org/obo/GENEPIO_0000113"^^ . "obsolete: NCBI BioSample attribute package"@en . "true"^^ . . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/GENEPIO_0000025"^^ . "http://purl.obolibrary.org/obo/GENEPIO_0000028"^^ . "obsolete: host sample material"@en . "true"^^ . . . . "Damion Dooley"@en . "food specimen detail"@en . . . "patient specimen"@en . . . "environmental"@en . "NCBI Biosample: environmental (swab or sampling)"@en . "environmental specimen"@en . . . . "A specimen extracted from an animal"@en . "Damion Dooley"@en . "animal specimen"@en . . . "built environment specimen"@en . . . "food specimen"@en . . . "natural environment specimen"@en . . . . "The type of person a patient had epidemiological (i.e. close proximity) contact with."@en . "Damion Dooley"@en . "exposure event person"@en . . . . "Damion Dooley"@en . "An exposure group statistics record is a sumary of disease outbreak statistics on a certain date of a group of humans or animals potentially exposed to a pathogen."@en . "exposure group statistics record"@en . . . . "symptom history item"@en . . . . "Damion Dooley" . "health state record"@en . . "http://purl.obolibrary.org/obo/NCIT_C17627" . "obsolete: swab"@en . "true"^^ . . "[WHICH DEFINITION?] See http://medical-dictionary.thefreedictionary.com/aspirate"@en . "Damion Dooley" . . "obsolete: fluid - aspirate"@en . "true"^^ . . _:genid112 . _:genid113 . _:genid114 . _:genid113 _:genid114 . _:genid114 . _:genid112 _:genid113 . _:genid112 . . . "Plant rinse is a rinse derived from plant material from one or more plants."@en . "Damion Dooley"@en . "plant rinse"@en . . . "Damion Dooley" . "outbreak animal exposure event location"@en . . . "Damion Dooley" . "animal exposure process"@en . . . "Damion Dooley" . "animal exposure event by material"@en . . . "Damion Dooley" . "exposure by human contact"@en . . "Damion Dooley" . "unnecessary distinction"@en . . "obsolete: human exposure activity type"@en . "true"^^ . . . "Damion Dooley" . "outbreak human exposure event location"@en . . . . "A process in which one or more humans may be exposed to one or more contagious human infectious disease carriers."@en . "Damion Dooley" . "human to human exposure process"@en . . . "water exposure by source"@en . . . "human water activity"@en . . . "This list would be customized to include organizations local to an application's software installation. It is an example of a set of ontology terms that would best be organized by a central authority if federated installations need to share investigator contact info for example."@en . "health authority"@en . . . "order:\nHP:0000118 # symptom\nFLU:0000976 # onset\nGENEPIO:0001789 # cessation\nGENEPIO:0001784 # duration" . . "Damion Dooley" . "symptom record"@en . . . _:genid115 . _:genid115 . _:genid115 . _:genid115 . "A visual pattern caused by DNA fragments concentrated in stratefied bands in a Pulsed-field gel electrophoresis (PFGE) gel plate."@en . "PFGE pattern"@en . . . . "phage type salmonella (DT)"@en . . . . "phage type e-coli 0157 (PT)"@en . . . . "Damion Dooley" . "sequence record"@en . . . . "A type of built structure that is suspected to be related to an outbreak investigation."@en . "Damion Dooley"@en . "outbreak exposure event location"@en . "http://purl.obolibrary.org/obo/ENVO_00000070" . . . . "Damion Dooley" . "lab test history record"@en . . . "obsolete: earth surface"@en . "true"^^ . . . . "A data specification is a specification of a data structure that can hold a categorical, textual or numeric variable, or that has such variables or other data structures as component parts."@en . "A data standard, may be defined as a data specification, but a data specification isn't necessarily a formal or de-facto data standard - it would have to be sanctioned by a community of users and developers to take on that status."@en . "Damion Dooley"@en . "data specification"@en . . . . . . "A specimen history item is a time-related datum about a particular specimen"@en . "Damion Dooley" . "specimen history item"@en . . . . "Damion Dooley"@en . "diagnostic test"@en . . "Damion Dooley"@en . "obsolete: sample datum"@en . "true"^^ . . "A laboratory sequencing datum is a datum related to the sequencing assay process applied to an isolate."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/GENEPIO_0001681"^^ . "obsolete: laboratory sequencing datum"@en . "true"^^ . . . "genomic sequencing annotation datum"@en . . . . "Damion Dooley" . "ISSUE: lab test results are appropriate to lab test types. Logic around that?"@en . "lab test record"@en . . . _:genid116 . _:genid116 . _:genid116 . _:genid116 . "sequencing assembly datum"@en . . . . "A container id is an identifier that refers to a container object about a patient specimen. Container ids are referenced in clinical patient records reported to be suspect, or lab test results."@en . "Damion Dooley" . "container record"@en . . . "Damion Dooley"@en . "identifier of a person with the context of a health care system"@en . "health care personal identifier"@en . . . _:genid117 . _:genid117 . _:genid117 . _:genid117 . . "A strain identifier is the unique microbial or eukaryotic strain name from a reference database that a sample has been matched to."@en . "Damion Dooley"@en . "strain identifier"@en . . . . "A line list is a collection of suspected or known disease outbreak cases. It may also include details about healthy patients associated with an exposure event (picnic, concert etc.) who have been interviewed in order to compare food intake, assess risk factors, etc. \n\nNote that the health status of people associated with an exposure event can change from healthy or unknown status, to ill patient."@en . "Damion Dooley" . "line list object"@en . . . "This class is a temporary holding bin for items that need a class hierarchy home, definition, and/or subclass items. Some classes have subclasses that are currently disjoint in other ontologies like ENVO, so awaiting resolution on such issues."@en . "Damion Dooley" . "awaiting ontology review"@en . . . "The IRIDA user ID is a user account identifier provided by the IRIDA.ca system."@en . "Damion Dooley" . . . "The count of healthy individuals or animals on a certain date/time from a group that was likely exposed to a pathogen"@en . "Damion Dooley" . "exposure group healthy count"@en . . . "The count of ill individuals or animals on a certain date/time from a group that was likely exposed to a pathogen"@en . "Damion Dooley" . "exposure group ill count"@en . . . "human general activity"@en . . . . "Damion Dooley" . "An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value."@en . "exposure history record"@en . . . . "Damion Dooley" . "isolate history record"@en . . . . "Damion Dooley" . "An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet)."@en . "outbreak history record"@en . . . . "Damion Dooley" . "Needs to cover the various pregnancy events"@en . "pregnancy history record"@en . . . . "Damion Dooley" . "Issue: a diagnosis is a set of diseases, each of which can be marked primary or secondary \"Illness causality\" with respect to a particular case? Requires a relation annotation."@en . "diagnosis record"@en . . . . "Damion Dooley" . "exposure event record"@en . . . . "Damion Dooley" . "hospitalization event record"@en . . . "An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value."@en . "exposure history item"@en . . . "hospital admission date"@en . . . "A date-time datum that marks the end of possible human or animal exposure to a pathogen agent, directly or indirectly."@en . "Damion Dooley" . "exposure event end"@en . . . "A date-time datum that marks the start of a human or animal exposure event to a suspected pathogen agent, directly or indirectly."@en . "Damion Dooley" . "This datum is NOT predicted as a function of pathogen and first symptom date."@en . "exposure event start"@en . . . "hospitalization history item"@en . . . "isolate history item"@en . . . "An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet)."@en . "outbreak history item"@en . . . _:genid118 . _:genid118 . _:genid118 . _:genid118 . "hospital discharge date"@en . . . . "A notification date is the date that an outbreak is suspected by a laboratory or other agency and is reported per outbreak detection guidelines."@en . "Damion Dooley" . "notification date"@en . . . . "An outbreak date is on which disease onset appears to have occured"@en . "Damion Dooley" . "outbreak date"@en . . . _:genid119 . _:genid119 . _:genid119 . _:genid119 . . "An outbreak over date is the date on which a disease outbreak appears to have abated"@en . "Damion Dooley" . "outbreak over"@en . . . . "test history item"@en . . . . "lab test result date"@en . . . "requires discussion"@en . "A data item that is a set of entities, referenced by mention, that don't necessarily have something in common."@en . "0000-0002-8844-9165"@en . "0000-0002-9578-0788" . "2022-01-31T03:45:04Z"^^ . "While \"enumeration\" is a \"data item\" not everything referenced within an enumeration qualifies as a \"data item\". Not to be confused with \"data set\" which describes \"data item\"s of the same type that have something in common."@en . "enumeration" . . . "An analytic datum which describes the observed or detectable signs, and experienced symptomps of an illness, injury, or condition."@en . "0000-0002-9578-0788" . "https://en.wikipedia.org/wiki/Signs_and_symptoms" . "2022-01-31T23:08:50Z"^^ . "signs & symptoms"@en . "signs and symptoms" . . . . "A particular attribute (feature, quality or process history) of a food sample."@en . "Damion Dooley"@en . "The underlying facets will be supplied from the FoodOn food ontology."@en . "food specimen datum"@en . . . "order:\nFOODON:03411564 # food source\nFOODON:00002381 # food product by organism\nFOODON:03311737 # processed food product\nNCIT:C71898 # brand name" . . "A food specimen type is a categorization of a food specimen, by the organism it is or came from, or by a class of food products."@en . "Damion Dooley"@en . "food specimen specification"@en . . . . "An agency that has reported a disease cluster."@en . "Damion Dooley"@en . "disease cluster notification agency"@en . . "This is a subset of OBI investigation identifier. It pertains only to NCBI Biosample projects"@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/OBI_0001628" . "obsolete: NCBI BioProject ID"@en . "true"^^ . . . "The count of individuals or animals for which no health status is available on a certain date/time from a group that was likely exposed to a pathogen."@en . "Damion Dooley" . "exposure group unknown health status count"@en . . _:genid120 . _:genid121 . _:genid123 _:genid122 . _:genid121 _:genid123 . _:genid122 . _:genid122 . _:genid122 . _:genid123 . _:genid120 _:genid121 . _:genid120 . . . "A role which inheres in a person and is realized by the process of being in the context of civilization"@en . "Damion Dooley"@en . "person role"@en . . . "An exposed person role is the role a person takes on who has been exposed to a pathogen. In serious situations this may call for special treatment, e.g. quarantine."@en . "Damion Dooley" . "exposed person role"@en . . . "parent-guardian role"@en . . . . "Damion Dooley" . "illness causality"@en . . . "pre-existing condition"@en . . . _:genid124 . _:genid124 . _:genid124 . _:genid124 . . "To restore to the normal state after some pathologic process."@en . "Damion Dooley" . "Dorland's Illustrated Medical Dictionary, 30th ed."@en . "improving"@en . "recovering"@en . "resolving health trend"@en . . . "Damion Dooley" . "close interpersonal relationship exposure"@en . . . "Damion Dooley" . "household exposure"@en . . . "Damion Dooley" . "exposure to individual with diarrhea"@en . . . "Damion Dooley" . "other human exposure"@en . . . "Damion Dooley" . "sexual contact exposure"@en . . . "Damion Dooley" . "exposure via diaper changing (human fecal)"@en . . . "container identifier"@en . . . "PulseNet: Outbreak" . "outbreak identifier"@en . . . . _:genid125 . _:genid125 . _:genid125 . _:genid125 . _:genid126 . _:genid126 . _:genid126 . _:genid126 . "GENEPIO"@en . "reference genome size"@en . . . _:genid127 . _:genid127 . _:genid127 . _:genid127 . . "The assembly genome size is the sum of all lengths of a sequence assembly's contigs."@en . "Damion Dooley"@en . "GENEPIO"@en . "As noted in Quast documentation: \" The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. \""@en . "assembly genome size"@en . . . . _:genid128 . _:genid128 . _:genid128 . _:genid128 . "Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community"@en . "Damion Dooley" . "GENEPIO"@en . "reference genome identifier"@en . . . "Assembly QC"@en . . "The 'genome size delta ratio' is a ratio of the difference between a sample's genome assembly size and the size of a given reference genome, over the reference genome size. \n\nThe formula:\n\n| (reference_genome_size - assembly_genome_size) | / reference_genome_size\n\nThis yeilds a decimal / percentage ranging from 0 = exact length, to say .1 which is equivalent to a 10% variance. If the ratio is too far from a quality control ratio that depends on the species in question, this indicates a bad assembly or a mis-identified sample."@en . "Damion Dooley"@en . "GENEPIO"@en . "genome size delta ratio"@en . . . "Assembly QC"@en . . "This is the upper acceptable limit of the 'genome size delta ratio' with respect to a particular species.\n\nFor Salmonella a 0.10 variance in length between an assembly size and a reference genome size may be acceptable. For E-coli a more generous 0.30 or .40 variance should be allowed, given the pathogenic subspecies\u2019 highly dynamic genome."@en . "GENEPIO"@en . "genome size delta ratio QC threshold"@en . . . "Assembly QC"@en . "http://purl.obolibrary.org/obo/IAO_0000428"@en . "The contig N50 length QC threshold is a minimum length threshold that a contig N50 length datum should be above for good QC. A lower length is indicative of assembly problems (insufficient read depth) or a mismatched reference genome."@en . "Damion Dooley"@en . "GENEPIO"@en . "contig N50 length QC threshold"@en . . . "Assembly QC"@en . "2000"^^ . . "The contig N99 length QC threshold is the minimum length that a contig N99 or NG99 length datum can be for satisfactory QC. This threshold avoids having too many gene coding regions prematurely clipped inside short contigs. An assembly having 1% or more of its content in less than 2Kbp chunks is cause for concern. Bacterial genes are generally about 1Kbp in length."@en . "Damion Dooley" . "GENEPIO"@en . "contig N99 length QC threshold"@en . . . _:genid129 . _:genid129 . _:genid130 . _:genid131 . _:genid132 . _:genid131 _:genid132 . _:genid133 . _:genid132 _:genid133 . _:genid133 . _:genid130 _:genid131 . _:genid129 _:genid130 . _:genid129 . "lookup" . "Homo sapiens"@en . . "The species of the host organism from which a specimen (pathogen) organism was obtained. Use the full taxonomic name, eg, \"Homo sapiens\"."@en . "Damion Dooley" . . "subject organism (host) taxonomic species"@en . _:genid134 . _:genid134 . _:genid134 . _:genid135 . _:genid135 . _:genid136 . _:genid137 . _:genid138 . _:genid137 _:genid138 . _:genid139 . _:genid138 _:genid139 . _:genid139 . _:genid136 _:genid137 . _:genid135 _:genid136 . _:genid134 _:genid135 . _:genid134 "lookup" . . . _:genid140 . _:genid140 . _:genid140 . _:genid140 . "Assembly QC"@en . . "A single datum having to do with a metric for genomic sequence assembly quality control. \n\nA \"quality control measurement\" can be defined as a measurement that has some norm within a definable context, e.g. for a certain subspecies. It may be a calculated quantity.\n\nA \"quality control metric\" is an upper or lower bound threshold that a measurement is compared to. Surpassing the threshold may indicate an error situation.\n\nA \"measure\" can indicate an amount of activity, consumption, transformation, etc. but doesn't itself convey an over-stepping of bounds in the way that a metric does."@en . "Damion Dooley" . "GENEPIO"@en . "assembly quality control datum"@en . . . _:genid141 . _:genid141 . _:genid141 . _:genid141 . _:genid142 . _:genid142 . _:genid142 . _:genid142 . "Damion Dooley"@en . "GSCID-BRC:Clinical/host-associated pathogen" . "NCBI:Pathogen.cl" . "clinical or host-associated pathogen"@en . _:genid143 . _:genid143 . _:genid143 . _:genid144 . _:genid144 . _:genid144 . _:genid143 _:genid144 . _:genid143 "Clinical/host-associated pathogen"@en . _:genid145 . _:genid145 . _:genid145 . _:genid146 . _:genid146 . _:genid146 . _:genid145 _:genid146 . _:genid145 "Pathogen.cl"@en . . . "Assembly QC"@en . "http://purl.obolibrary.org/obo/IAO_0000428"@en . "The N99 length definition is identical to the N50 definition except that the threshold for determining the contigs is 1% of the nucleotides. This contig basepair length can be compared to a minimum threshold to determine if gene annotation (where contigs greater than say 2000bp are necessary) would generally succeed."@en . "Damion Dooley"@en . "GENEPIO"@en . "contig N99"@en . . . "Assembly QC"@en . "http://purl.obolibrary.org/obo/IAO_0000428" . "The upper threshold of contig counts that are acceptable in a genome assembly. This may vary based on the overall genome length and depth of coverage.\n\nA large contig count may indicate insufficient read coverage."@en . "Damion Dooley"@en . "contig count QC threshold"@en . . . . "Indicates how the knowledge derived from the project can be applied, and to what field(s)."@en . "Damion Dooley's note: NAIAD GRCID-BRC has Project Relevance map to OBO Foundry Study Design (http://purl.obolibrary.org/obo/OBI_0500000) but this is a bit of a stretch."@en . "Damion Dooley" . "https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project"^^ . "project relevance"@en . . . "agricultural project relevance"@en . . . "medical knowledge relevance"@en . . . "industrial processing relevance"@en . . . "evolution modelling relevance"@en . . . "environmental project relevance"@en . . . "model organism relevance"@en . . "The NCBI BioProject model includes all datums associated with the current NCBI BioProject specification."@en . "Damion Dooley"@en . . "obsolete: NCBI BioProject model"@en . "true"^^ . . "http://purl.obolibrary.org/obo/GENEPIO_0000147" . "obsolete: NCBI SRA model"@en . "true"^^ . . . "http://www.ncbi.nlm.nih.gov/biosample/docs/attributes/"@en . "http://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/"@en . . "Damion Dooley notes: NCBI doesn't quite make the distinction but it may be helpful to distinguish sample submission facilitator vs submitter/repository organization contact? So should we have a\nBioSample_submission_facilitator field and a BioSample_contact_information field?"@en . "Damion Dooley" . "Damion's note: There are a few different kinds of biosample, and required fields depend on the type selected."@en . "draft NCBI BioSample model - mixed clinical and environmental/food/other"@en . . . "monoisolate"@en . . "A monoisolate sample scope involves specimens from a single animal, cultured cell-line, inbred population, or possibly a heterogeneous population when a single genome assembly is generated from a pooled sample because multiple individuals are needed to collect enough material and an inbred line is not available; however, this situation is not preferred."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/" . "monoisolate" . "monoisolate sample scope"@en . . . "multiisolate"@en . . "A multiisolate sample scope contains multiple individuals that represent distinct specimen collections, a population (representative of a species)."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"@en . "This is often used for variation or phenotype and genotype studies. This should not be used when multiple genomes will be annotated. Eventually, multiple locus_tag prefixes will be able to be assigned to a single multiisolate genome sequencing project, but currently only a single prefix can be registered per project. Therefore, individual monoisolate projects need to be registered when more than one genome will be annotated."@en . "multiisolate sample scope"@en . . . "multispecies"@en . . "A multi-species sample scope involves a sample representing multiple species."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/" . "multispecies sample scope"@en . . . "environment"@en . . "An environment sample scope indicates that the species content of the sample is not known. Generally, nucleic acid is directly isolated from an environmental sample for analysis. This is used for metagenome studies."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/" . "environment sample scope"@en . . . . "A synthetic sample scope involves a sample synthesized in a laboratory."@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/" . "synthetic sample scope"@en . . . . "Damion Dooley"@en . "single cell"@en . . . "other"@en . . "Other project objective: specify an objective not listed above"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "other project objective"@en . . . _:genid147 . _:genid147 . _:genid147 . _:genid147 . _:genid148 . _:genid148 . _:genid148 . _:genid148 . "Damion Dooley"@en . "GSCID-BRC:environmental/food/other" . "NCBI:Pathogen.env" . "environmental, food or other pathogen"@en . _:genid149 . _:genid149 . _:genid149 . _:genid150 . _:genid150 . _:genid150 . _:genid149 _:genid150 . _:genid149 "environmental/food/other"@en . _:genid151 . _:genid151 . _:genid151 . _:genid152 . _:genid152 . _:genid152 . _:genid151 _:genid152 . _:genid151 "Pathogen.env"@en . . . "whole"@en . . "Whole: the project makes use of the whole sample material (most common case). Use this for whole genome sequencing studies, transcriptome studies that are not targeting specific loci, epigenetic studies of a genome, and metagenomes or unbiased transcriptome studies of metagenomes."@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "whole genomic data capture"@en . . . "raw sequence reads"@en . . "A raw sequence reads project objective has the goal of submission of raw reads to SRA or Trace repositories"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "raw sequence read objective"@en . . . "sequence"@en . . "A sequence project objective has a goal of submission of sequence data to standard archival sequence databases (yielding accession.version identifiers; e.g., whole genome shotgun, cDNA sequences, transcript shotgun assemblies)"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "sequence project objective"@en . . . "analysis"@en . . "An \"analysis project objective\" indicates there was an other analysis not otherwise indicated, includes submission of BAM files."@en . "This defn. could be a negation of the \"not otherwise indicated\"."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "analysis objective"@en . . . "assembly"@en . . "Submission of genome assembly (AGP data)"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "assembly objective"@en . . . "annotation"@en . . "Sequence annotation data"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "sequence annotation objective"@en . . . "sequence variation"@en . . "Variation: identification of sequence variation data for submission to dbSNP or dbVAR"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "sequence variation project objective"@en . . . "epigenetic markers"@en . . "DNA methylation, histone modification, chromatin accessibility datasets"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "epigenetic markers objective"@en . . . "expression"@en . . "Expression: assays of transcript or protein existence or abundance"@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "transcript or protein expression objective"@en . . . "maps"@en . . "Maps: non-sequence based map data; e.g., genetic, radiation hybrid, cytogenetic, etc."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "mapping objective"@en . . . . "Phenotypic descriptive data."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "phenotypic observation data from specimen"@en . . . "select sequence if any sequence data is generated from this project."@en . "sequencing"@en . . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "sequencing project method"@en . . . "array"@en . . "Select Array if that is the primary method and no sequence data is submitted"@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "array project method"@en . . . "mass spectrometry"@en . . "Select Mass Spectrometry if that is the primary method"@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "mass spectrometry project method"@en . . . "order:\nNCIT:C40974 # first name\nNCIT:C40975 # last name\nNCIT:C42775 # email address\nGENEPIO:0001756 # phone" . "contact specification - person"@en . . . "A categorical investigation datum is a datum pertaining to some entity examined for scientific research or diagnostic purposes and which has a scope that is broader than one of the clinical, environmental or epidemiological domains."@en . "Damion Dooley"@en . "investigation datum"@en . . . "An organism and its host share physical space but no evidence exists to determine if one benefits from this arrangement."@en . "commensal role"@en . . . "draft isolate details model"@en . . . . "A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time."@en . "Damion Dooley"@en . "subject age"@en . . . . "draft NCBI component model"@en . . . "draft IRIDA BioSample model"@en . . . _:genid153 . _:genid153 . _:genid153 . _:genid153 . "draft GenEpiO epidemiology case record"@en . . . _:genid154 . _:genid154 . _:genid154 . _:genid154 . "A subject description is a field containing additional information about an organism (related to an investigation, study and/or specimen) that is not included in other defined vocabulary fields."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/GENEPIO_0001835"^^ . "subject description"@en . _:genid155 . _:genid155 . _:genid155 . _:genid156 . _:genid156 . _:genid156 . _:genid155 _:genid156 . _:genid155 "host description"@en . . . "NCBI BioSample"@en . "The host profile or identifiers text is the \"identification or description of the specific individual from which this sample was obtained\"."@en . "Damion Dooley"@en . "NCBI BioSample: isolate" . "host profile or identifers"@en . . . . "A subject identifier is an identifier of a subject organism within the context of a particular investigation, study, or specimen extraction event."@en . "Damion Dooley"@en . "This varies in its type (numeric or string) and its central repository depending on its context (use in a particular application/instance).\n\nNote: GSCID-BRC specification states \" 'Host' is not the preferred term since some specimens may lack any detectable pathogen\". In other words, a person would technically (logically) only have a host identifier AFTER they have been diagnosed as having a pathogen. A health care personal identifier, or a case identifier would be better than a more ephemeral \"host id\""@en . "subject identifier"@en . . . _:genid157 . _:genid157 . _:genid157 . _:genid157 . . "Name of disease in a subject that is related to a given investigation, study and/or specimen."@en . "Damion Dooley"@en . "NIAID GSCID-BRC metadata working group"@en . "Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID\nor https://www.ncbi.nlm.nih.gov/mesh/1000067"@en . "subject disease"@en . . . "INSDC term (top level)"@en . "A categorical choice recorded when a measurement value was known to be recorded in the past but the observed value cannot be located or retrieved for some reason."@en . . . "NCBI Biosample: missing"@en . "missing"@en . . . "INSDC term (top level)"@en . "'not applicable' is an appropriate value for the measure of femur length for a patient with a missing limb"@en . . "A categorical choice recorded when a measurable datum does not apply to a given context."@en . "Damion Dooley"@en . . . . "not applicable"@en . . . "INSDC term (lower level)" . "A categorical choice recorded when a datum was not measured with respect to some entity during some process."@en . . . "NCBI Biosample: not collected"@en . "not collected"@en . . . "draft isolate identifier model"@en . . . . "draft GenEpiO isolate testing model"@en . . . . "draft NCBI isolate source location model"@en . . . "draft GenEpiO isolate environment model"@en . . . "A subject disease stage is a measure of the acuteness of a subject organism's diagnosed disease, if any, at a given time in an investigation, study or specimen extraction event."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/GENEPIO_0001835"^^ . "subject disease stage"@en . . . "environmental datum"@en . . . _:genid158 . _:genid158 . _:genid158 . _:genid158 . "temperature of sample"@en . . . . "de-novo assembly"@en . . . "http://purl.obolibrary.org/obo/GENEPIO_0000025"^^ . "obsolete: sample body source"@en . "true"^^ . . . "contig pre-analysis minimum length QC threshold"@en . . "A 'contig length QC threshold' is an integer setting which can be applied by an algorithm to an array of assembly and annotation contig lengths to remove (filter out) all items less than the threshold value. The reduced array is used for calculation of statistics."@en . "Damion Dooley"@en . "http://quast.bioinf.spbau.ru/manual.html"@en . "QUAST specifies which of its report stats are affected by the \"--min-contig\" minimum contig length parameter."@en . "contig length QC threshold"@en . . . . "The NG50 length is the same as the N50 length except that the length of the reference genome is used in the calculation rather than the assembly genome size."@en . "Damion Dooley" . "\"Note that N50 is calculated in the context of the assembly size rather than the genome size. Therefore, comparisons of N50 values derived from assemblies of significantly different lengths are usually not informative, even if for the same genome. To address this, the authors of the Assemblathon competition derived a new measure called NG50. The NG50 statistic is the same as N50 except that it is 50% of the known or estimated genome size that must be of the NG50 length or longer. This allows for meaningful comparisons between different assemblies. In the typical case that the assembly size is not more than the genome size, the NG50 statistic will not be more than the N50 statistic.\" - wikipedia"@en . "contig NG50"@en . . . _:genid159 . _:genid159 . _:genid159 . _:genid159 . . "A contig length is the count of base pairs in a given sequence assembly contig."@en . "Damion Dooley" . "contig length"@en . . . "Assembly QC" . "http://purl.obolibrary.org/obo/IAO_0000428" . "Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation."@en . "Damion Dooley"@en . "QUAST manual"@en . "contig L50"@en . . . "Assembly QC" . "http://purl.obolibrary.org/obo/IAO_0000428" . "The LG99 count is like the L99 count except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths."@en . "Damion Dooley"@en . "contig LG99"@en . . . "An organism isolate datum is any datum pertaining to an isolate organism"@en . "Damion Dooley" . "obsolete: specimen from subject datum"@en . "true"^^ . . . _:genid160 . _:genid160 . _:genid160 . _:genid160 . . "A product of an animal, as in blood, feces, sputum, etc. that has no particular anatomical site"@en . "Damion Dooley" . "animal body product"@en . . "This is the scientific role or category that the subject organism or material has with respect to an investigation."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/GENEPIO_0001237"^^ . "obsolete: specimen source material category"@en . "true"^^ . . . "draft GenEpiO general information record"@en . . . _:genid161 . _:genid161 . _:genid161 . _:genid161 . _:genid162 . _:genid162 . _:genid162 . _:genid162 . "An antigenic formula is a string composed of codes representing categorized results of tests performed on various viral, bacterial or immune cell surface antigens."@en . "Damion Dooley" . "antigenic formula"@en . "http://medical-dictionary.thefreedictionary.com/antigen" . . . _:genid163 . _:genid163 . _:genid164 . _:genid165 . _:genid166 . _:genid165 _:genid166 . _:genid167 . _:genid166 _:genid167 . _:genid168 . _:genid167 _:genid168 . _:genid168 . _:genid164 _:genid165 . _:genid163 _:genid164 . _:genid163 . "lookup" . . "This is the taxonomic species descriptor of a specimen isolate (an organism found within a specimen.)"@en . "Damion Dooley"@en . "specimen organism taxonomy (species)"@en . . . . "An identifier moe3l indicates an identifier, the organization it has been issued by, and the status of the identifier - whether it is a primary one, active or archaic."@en . "Damion Dooley" . "identifier model"@en . . . "help:This should be populated with a selection from INSDC.org controlled vocabulary for providers: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt"@en . . "The curator organization name is the name of an organization that manages a given repository of entities (samples, isolates, sequences ...)"@en . "Damion Dooley"@en . "curator organization name"@en . . . "INSDC:institution_code:BRS"@en . "IRIDA:ACK" . "Agriculture and Agri-Food Canada" . . . . "An isolate identifier is an identifier assigned to a given isolate by a particular agency that is handling or storing it."@en . "Damion Dooley"@en . "isolate identifier"@en . . . . "An identifier status describes the principle role of an identifier assigned to an entity by its curator or handler. An entity may have a number of identifiers assigned to it over time. An identifier may be phased-out as can happen when its content is transferred to another curator."@en . "Damion Dooley"@en . "identifier status"@en . . . "GenEpiO"@en . . "A data protection role is a role (or user permission) that a user has with respect to particular data."@en . "A data server may be able to provide a protected(modified) dataset with metadata indicating what parts have a protection role with respect to the user requesting this information. A data protection role would be inherited from a user's relation to an entitiy to the entity's components or subclasses."@en . "Damion Dooley"@en . "data protection role"@en . . . . . "An identifier used in the initial submission of content to a repository."@en . "original submission"@en . . . . "This was created to help define a contributing organization to a repository. However this still needs organizing. The \"collected_by\" field is free text but contact name AND organization could be associated with this in controlled vocabulary."@en . "NCBI Contributing organization / project"@en . . . "food - liquid"@en . . . . "draft NCBI BioSample identifier model"@en . . . . "An INSDC institution code is an identifier of an organization from a list of sequence repository organizations managed by INSDC."@en . "Damion Dooley" . "http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier"^^ . "INSDC institution code"@en . . . "draft IRIDA epidemiological case model"@en . . . . "An identifier that had been used previously but is no longer promoted."@en . "Damion Dooley" . "previous (archaic) identifier"@en . . . . "A geographical location datum is a datum that refers to a real, hypothesized or fanciful spatial location"@en . "Damion Dooley" . "geographic location datum"@en . . "A categorical tree specification datum is a categorical value specification which takes its value from the ontology URI identifier of any one of its subclass items; these may be organized in a hierarchy."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/OBI_0001930"^^ . "A categorical tree specification datum may have its own URI identifier as its value. This could be interpreted to mean that the datum was recorded but that no particular categorical subclass distinction was observed. This in effect makes the datum act as a boolean variable."@en . "obsolete: categorical tree specification"@en . "true"^^ . . . . "Damion Dooley"@en . "A geographic coordinate entity composed of both latitude and longitude components."@en . "latitude and longitude coordinate (ISO 6709)"@en . . . _:genid169 . _:genid169 . _:genid169 . _:genid169 . "order:\nNCIT:C25464 # country\nENVO:00000005 # state / province etc."@en . . "Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg \"Canada: Vancouver\" or \"Germany: halfway down Zugspitze, Alps\""@en . "Damion Dooley" . "draft NCBI BioSample geo_loc_name model"@en . . . "draft GenEpiO isolate sequencing model"@en . . . "A case ID is a unique identifier associated with a particular episode of care for an individual or animal." . "Damion Dooley" . "case identifier"@en . . . . . "An animal that has had a substantial part of its reproductive organs removed surgically."@en . "Damion Dooley" . "NCBI BioSample: neuter" . "Not a PATO phenotypic sex catigorical value."@en . "neuter"@en . . _:genid170 . _:genid171 . _:genid172 . _:genid171 _:genid172 . _:genid172 . _:genid170 _:genid171 . _:genid170 . . "NCBI BioSample" . "'pooled male and female' is a categorical value used when the male and female categories or levels of a factor are combined. If used to describe a single organism, then the organism will be one or the other."@en . "Not a PATO phenotypic sex catigorical value."@en . "Damion Dooley" . "NCBI BioSample: 'pooled male and female'" . "pooled male and female"@en . . . . "A categorical choice recorded while the data for a given measurable datum has not finished being collected, is awaiting a conclusion, or has not yet been communicated."@en . "Damion Dooley"@en . "undetermined"@en . "in process"@en . . . "swimming / wading"@en . . . . "Damion Dooley" . "NECESSARY? : What details are categorical and what are freehand? This item was originally too broad; moved sub-items to Treatment."@en . "infection detail datum"@en . . . . "This is problematic - its not clear if this is reporting that antibiotics were administered, or whether they are recommended as a result of diagnosis."@en . "Damion Dooley" . "antibiotics required"@en . . . . "The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations."@en . "Damion Dooley" . "International Nucleotide Database Collaboration standard"@en . "INSDC" . "INSDC standard"@en . . . . "Damion Dooley" . "outcome of pregnancy associated with illness"@en . . . "INSDC term (lower level)" . "a categorical choice indicating that information of an expected format was not given; a value may be given at the later stage."@en . . . "not provided"@en . . . _:genid173 . _:genid173 . _:genid173 . _:genid173 . _:genid174 . _:genid174 . _:genid174 . _:genid174 . . "Damion Dooley" . "stable health status"@en . "http://purl.obolibrary.org/obo/GENEPIO_0002026"@en . . . "induced abortion"@en . . . . "live birth"@en . . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/VT_0002292"^^ . "obsolete: gestation duration (weeks)"@en . "true"^^ . . . _:genid175 . _:genid175 . _:genid175 . _:genid175 . "date of pregnancy outcome"@en . . . _:genid176 . _:genid176 . _:genid176 . _:genid176 . _:genid177 . _:genid177 . _:genid177 . _:genid177 . . "contact specification - physician"@en . . "obsolete: matrix - solid"@en . "true"^^ . . . _:genid178 . _:genid178 . _:genid178 . _:genid178 . . "contact specification - parent/guardian"@en . . . _:genid179 . _:genid179 . _:genid179 . _:genid179 . _:genid180 . _:genid180 . _:genid180 . _:genid180 . . "contact specification - patient"@en . . . "draft GenEpiO case epidemiology record"@en . . . "order:\nNCIT:C25464 # Country\nENVO:00000005 # major administrative subdivision aka state/province/territory/region (via GenEpiO -> GAZ )\nNCIT:C80234 # Municipality (via GenEpiO -> GAZ cities)\nNCIT:C25690 # Street Address\nNCIT:C25621 # postal code" . . "The address component of a contact specification."@en . "contact specification - address"@en . . . "GENEPIO_0001829"@en . "obsolete: draft IRIDA model"@en . "true"^^ . . . . "A datum related to the sequencing assay process applied to an isolate."@en . "Damion Dooley"@en . "laboratory sequencing datum"@en . "http://purl.obolibrary.org/obo/OBI_0001901"^^ . "http://purl.obolibrary.org/obo/OBI_0400103"^^ . . . . "Damion Dooley" . "host illness associated with"@en . . . "draft subject demographic specification"@en . . . _:genid181 . _:genid181 . _:genid181 . _:genid181 . _:genid182 . _:genid182 . _:genid183 . _:genid183 . _:genid185 _:genid184 . _:genid184 "K(1|2a|2ac|3|4|5|6|7|8|9|10|11|12|13|14|15|16|18a|18ab|19|20|22|23|24|26|27|28|29|30|31|34|37|39|40|41|42|43|44|45|46|47|49|50|51|52|53|54|56|96|55|74|82|84|85ab|85ac|87|92|93|95|97|98|100|101|102|103|X104|X105|X106)" . _:genid185 . _:genid183 _:genid185 . _:genid182 _:genid183 . _:genid182 . "E. coli K antigen specification"@en . . . _:genid186 . _:genid186 . _:genid186 . _:genid186 . _:genid187 . _:genid187 . _:genid187 "1"^^ . _:genid188 . _:genid188 . _:genid190 _:genid189 . _:genid189 "6"^^ . _:genid190 . _:genid188 _:genid190 . _:genid187 _:genid188 . _:genid187 . "other antigen specification"@en . . . . "E. coli serotype specification"@en . . . . "Damion's note: This will be converted to a categorical tree specification list of serovars by name or id asap."@en . "Salmonella serovar specification"@en . . . . "A lab test specification indicates the inputs and outputs (results / conclusions) of a test."@en . "Damion Dooley" . "test specification"@en . . . _:genid191 . _:genid191 . _:genid191 . _:genid191 . _:genid192 . _:genid192 . _:genid193 . _:genid193 . _:genid195 _:genid194 . _:genid194 "(1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7)" . _:genid195 . _:genid193 _:genid195 . _:genid192 _:genid193 . _:genid192 . "listeria antigen"@en . . "obsolete: matrix - fluid"@en . "true"^^ . . . "listeria serotype 1/2a"@en . . . "listeria serotype 1/2b"@en . . . "listeria serotype 1/2c"@en . . . "listeria serotype 1/2"@en . . . "listeria serotype 3a"@en . . . "listeria serotype 3b"@en . . . "listeria serotype 4a"@en . . . "listeria serotype 4b"@en . . . "listeria serotype 4c"@en . . . "listeria serotype 4d"@en . . . "listeria serotype 4e"@en . . . "non-monocytogenes listeria antigen"@en . . . "listeria serotype 3c"@en . . . "textual test result"@en . . "This is an organizational category for grouping parameters relevant to biomedical research projects."@en . "Damion Dooley" . . "obsolete: draft GenEpiO BioProject standard"@en . "true"^^ . . . "Damion Dooley" . "NCBI BioSample: collection_code" . "NCBI BioSample collection code"@en . . . _:genid196 . _:genid196 . _:genid196 . _:genid196 . . "draft NCBI BioSample host model"@en . . . "food - solid"@en . . . "lab test datum"@en . . . "Xbal"@en . . . "Ascl"@en . . . "Smal"@en . . . "Blnl"@en . . . "Apal"@en . . . "Kpnl"@en . . . . "Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate."@en . "Damion Dooley" . "NCBI Biosample"@en . "subgroup"@en . . . "help:This is an optional additional subtype classification as per organism convention"@en . . "A viral subtype is a classification name for a virus according to some protocol."@en . "Damion Dooley" . "NCBI BioSample"@en . "viral subtype"@en . . . _:genid197 . _:genid197 . _:genid197 "1"^^ . _:genid197 . _:genid197 . _:genid198 . _:genid198 . _:genid198 "1"^^ . _:genid198 . _:genid198 . . "serotype specification"@en . . . "IRIDA"@en . . "An integer and character referring to a pattern of opaque or confluent lysis caused by a panel of bacteriophage infections e.g. 14a."@en . "Damion Dooley"@en . "SNOMED: http://www.snomedbrowser.com/Codes/Details/272405002" . "phage type specification"@en . . . "obsolete: swab - food contact surface"@en . "true"^^ . . . "ATCC:26370" . "An NCBI culture collection is a composite identifier containing \u201Cinstitution code:collection code\u201D."@en . "Annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier."@en . "NCBI culture collection"@en . . . "UAM:Mamm:52179" . "The NCBI specimen voucher is an identifier composed of \u201Cinstitution code:collection code:specimen id\u201D parts. In addition to a specimen identifier, it includes an institution-code (and optional collection-code) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides."@en . "INSDC:specimen_voucher"@en . "NCBI specimen voucher"@en . "http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier."^^ . . . "culture identifier"@en . . . _:genid199 . _:genid199 . _:genid199 . _:genid199 . "human; dog; horse"@en . "The natural language (non-taxonomic) name of the type of organism (human or animal) that is the subject of a given investigation, study and/or specimen."@en . "Damion Dooley's note: as of 2017 this is a problematic field for NCBI Biosample because it is slotted into \"host\" field, yet field is listed as \"host common name\" which does not fit with requirement that scientific name be provided."@en . "Person: Damion Dooley" . "subject organism common name"@en . . . _:genid200 . _:genid200 . _:genid200 . _:genid200 . _:genid201 . _:genid201 . _:genid201 . _:genid201 . "temperature of air - average daily"@en . . . "obsolete: swab - inanimate object surface"@en . "true"^^ . . . "obsolete: swab - meat"@en . "true"^^ . . . "obsolete: swab - rectal swab"@en . "true"^^ . . . "obsolete: swab - tissue"@en . "true"^^ . . . "unknown source"@en . . . . "patient sample"@en . "human clinical specimen"@en . . "\"environment (swab or sampling)\" is a specific response for NCBI BioSample that could be mapped or unified with \"environment sample\" used elsewhere in GenEpiO"@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/GENEPIO_0001246"^^ . "obsolete: environmental (swab or sampling)"@en . "true"^^ . . . "avian - wild"@en . . . "avian - domesticated"@en . . . "human clinical specimen - invasive"@en . . . "In chemistry, pH is a numeric scale used to specify the acidity or basicity(alkalinity) of an aqueous solution"@en . "Damion Dooley"@en . "Wikipedia"@en . "Normally falls within the bounds of 0 - 14"@en . "pH measurement"@en . . . "precipitation"@en . . . . "The assembly and annotation objective is the set of objectives that assembly and annotation techniques (including instruments and software platforms) applied to a sample are meant to satisfy. This impacts on the quality control thresholds applied to the sequencing project."@en . "Damion Dooley" . "assembly and annotation project objective"@en . . . . "Damion Dooley" . "line list row record"@en . . . . "This class contains components under development for fulfilling GenEpiO and other standard data specifications. Components are relevant to epidemiological, laboratory, clinical or environmental pathogen sample data collection and analysis."@en . "Damion Dooley" . "draft GenEpiO component record"@en . . . . . . "region"@en . "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" . . "A subnational region is a type of subnational entity similar to a nation's state, province, or territory."@en . "Damion Dooley" . "subnational region"@en . . . . "A data standard related to public health research and service delivery."@en . "Damion Dooley"@en . "public health data standard"@en . . "Damion Dooley" . . . . "Reagent: material studied was obtained by chemical reaction, precipitation."@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "reagent derived material from specimen"@en . . . "transcriptome"@en . . "Transcriptome: transcript and/or expression data."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "transcriptome data from specimen"@en . . . "proteome" . . "Proteome material is protein or peptide sequences."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "proteome data derived from specimen"@en . . . "purified chromosome" . . "Purified chromosome: one or more chromosomes or replicons were experimentally purified."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "purified chromosome from specimen"@en . . . "targeted locus/loci"@en . . "TargetedLocusLoci: capturing specific loci (gene, genomic region, bar code standard)."@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "Targeted Locus Loci data capture"@en . . . "clone ends"@en . . "CloneEnds: capturing clone end data."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "clone end data capture"@en . . . "exome"@en . . "Exome: capturing exon-specific data."@en . "Damion Dooley"@en . "NCBI BioSample"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "exome specific data capture"@en . . . "random survey"@en . . "Sequences generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material"@en . "Is this with respect to an isolate or a specimen derived culture?"@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^ . "random survey data capture"@en . . . . "This is a collection of various human (and animal contact location) contact information specifications used in data standards."@en . "Damion Dooley"@en . "contact specification"@en . . . "order:\nNCIT:C40978 # phone\nGENEPIO:0001896 # phone type" . . "contact specification - phone"@en . . . . "Damion Dooley" . "millimetres per day"@en . . . "obsolete: millisiemens"@en . "true"^^ . . . . "Damion Dooley" . "millisiemens per centimetre"@en . . . . "Damion Dooley" . "cubic metre per second"@en . . . "umol/kg" . . "Damion Dooley" . "micromole per kilogram"@en . . . . "Damion Dooley" . "micromole per litre"@en . . . . "Damion Dooley" . "quality control record"@en . . . "Standard draft: describing the minimum information needed for submission to a public database."@en . "Damion Dooley" . "1 - standard draft"@en . . . "High quality draft: describing sequences with little to no manual review."@en . "Damion Dooley" . "2 - high quality draft"@en . . . "Improved high quality draft: in which data is either reviewed by people or machines to some extent to indicate that most of the genetic data is assembled correctly, but some errors may still be present."@en . "Damion Dooley" . "3 - improved high quality draft"@en . . . "Annotation-directed improvement: in which genetic information in various gene regions is represented as accurately as possible."@en . "Damion Dooley" . "4 - annotation-directed improvement"@en . . . "Non-contiguous finished: which includes sequences that have been reviewed by both people and machines and would be considered complete except for \u201Crecalcitrant regions\u201D that are proving problematic for genome closure."@en . "Damion Dooley" . "5 - non-contiguous finished"@en . . . "Finished: which describes un-gapped complete sequences that have minimal errors, if any. The biology of the microbe will determine whether this finished genome consists of more than one chromosome."@en . "Damion Dooley" . "6 - finished"@en . . . "Assembly QC"@en . "http://purl.obolibrary.org/obo/IAO_0000428"@en . "The NG99 length is the same as the N99 length except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths."@en . "Damion Dooley"@en . "GENEPIO"@en . "contig NG99"@en . . . "Assembly QC" . "http://purl.obolibrary.org/obo/IAO_0000428" . "Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation."@en . "Damion Dooley"@en . "contig LG50"@en . . . "Assembly QC" . "http://purl.obolibrary.org/obo/IAO_0000428" . "Contig L99 is the number of contigs equal to or longer than contig N99. The length of the assembly itself is used in the calculation."@en . "Damion Dooley"@en . "contig L99"@en . . . . "A subject age at time of specimen extraction is the age (since birth) of the organism at the time a given specimen was extracted."@en . "Damion Dooley"@en . "subject age at time of specimen collection"@en . . . . "A public health related data standard involving a particular species of pathogen."@en . "Damion Dooley"@en . "pathogen specific data standard"@en . . . . "The draft tuberculosis contextual data standard is a data standard for the collection of contextual information of a given tuberculosis case that pertain to typing, clinical treatment, and potential research questions."@en . "Damion Dooley" . "draft tuberculosis contextual data standard"@en . . . _:genid202 . _:genid202 . _:genid202 "1"^^ . _:genid203 . _:genid204 . _:genid206 _:genid205 . _:genid204 _:genid206 . _:genid205 . _:genid205 . _:genid205 . _:genid208 _:genid207 . _:genid206 _:genid208 . _:genid207 . _:genid207 . _:genid207 . _:genid210 _:genid209 . _:genid208 _:genid210 . _:genid209 . _:genid209 . _:genid209 . _:genid212 _:genid211 . _:genid210 _:genid212 . _:genid211 . _:genid211 . _:genid211 "PulseNet:Outbreak" . _:genid212 . _:genid203 _:genid204 . _:genid202 _:genid203 . _:genid202 . . "The PulseNet Canada Salmonella submission standard details the fields required in a PuseNet Canada pathogen submission report for Salmonella in spreadsheet format"@en . "Damion Dooley" . "draft PulseNet Canada Salmonella submission standard"@en . "http://www.pulsenetinternational.org/assets/PulseNet/uploads/wgs/PND18-NCBI-Biosample-Submission.pdf" . . . _:genid213 . _:genid213 . _:genid213 . _:genid213 . "A PFGE pattern resulting from DNA fragmentation induced by the Xbal enzyme."@en . . "PFGE Xbal pattern"@en . . . _:genid214 . _:genid214 . _:genid214 . _:genid214 . "A PFGE pattern resulting from DNA fragmentation induced by the Blnl enzyme."@en . . "PFGE Blnl pattern"@en . . . "NLEP ID"@en . "An NLEP ID is a unique identifier code for a sample registered with the Canadian \"National Laboratory for Enteric Pathogens\" (NLEP)"@en . "Damion Dooley" . "Pulsenet Canada spreadsheet."@en . "National Laboratory for Enteric Pathogens Identifier"@en . . . _:genid215 . _:genid215 . _:genid215 . _:genid215 . "PulseNet spreadsheet" . "Date an uploaded sample was re-uploaded or had its metadata modified."@en . "Damion Dooley" . "PulseNet: UploadModifiedDate" . "upload modified date"@en . . . . "A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip."@en . "Damion Dooley" . "travel destination"@en . . . . . "A symptom duration is a date-time entity which is the duration (in hours or days or weeks etc.) that one or more symptoms persist for in a particular human or animal"@en . "Damion Dooley" . "This may be a calculated field if symptoms are reported to cease on a particular date. Often however symptom duration is reported more generally as a date or time range since cesation date is less certain."@en . "symptom duration"@en . . . _:genid216 . _:genid216 . _:genid216 . _:genid216 . . "The city where a specimen was collected (taken) from a subject or environment"@en . "Damion Dooley" . "specimen collection location - city"@en . _:genid217 . _:genid217 . _:genid217 . _:genid218 . _:genid218 . _:genid218 . _:genid217 _:genid218 . _:genid217 "lookup" . . "Damion Dooley" . . . "obsolete: sample city"@en . "true"^^ . . . _:genid219 . _:genid219 . _:genid219 . _:genid219 . . "This is the genus-level taxonomic name of an organism playing a pathogen role"@en . "Damion Dooley" . "genus of pathogen"@en . . . _:genid220 . _:genid220 . _:genid220 . _:genid220 . . "This is the species-level taxonomic name of an organism playing a pathogen role"@en . "Damion Dooley" . "species of pathogen"@en . . . . "A symptom cessation date is a date-time entity that marks the end of one or more reported symptoms pertaining to an episode of human or animal illness"@en . "Damion Dooley"@en . "symptom cessation date"@en . . . _:genid221 . _:genid221 . _:genid221 . _:genid221 . "This is a catch-all category for listing specimen related terms"@en . "Damion Dooley"@en . "specimen datum"@en . . . . . . . . . . . . . "http://purl.obolibrary.org/obo/GENEPIO_0002105"@en . "http://purl.obolibrary.org/obo/OBI_0001616"^^ . . . _:genid222 . _:genid222 . _:genid222 . _:genid222 . . "isolate identifier specification"@en . . . . "The 'data obfuscated' role between a user and given data entails that the user is authorized to see particular fields that have been transformed consistently such that statistics performed on those fields would yeild the same results as statistics applied to the un-obfuscated data. The purpose of obfuscation is to prevent related individuals or organizations from being identified."@en . "Damion Dooley"@en . "data obfuscated"@en . "https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/"^^ . . . . "The 'data aggregated' role between a user and given data entails that the user is authorized to see aggregated results (like the patient count) via preset reports, queries or views. The results are not obfuscated."@en . "Damion Dooley" . "data aggregated"@en . . . . "A 'limited data set' role between a user and given data entails that a user is authorized to see some of the fields but the remainder are withheld (or encrypted)."@en . "Damion Dooley" . "limited data set"@en . . . "help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users."@en . . "A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them."@en . "Damion Dooley's note: There is a case in the \"draft tuberculosis contextual data standard\" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature."@en . "Damion Dooley" . "Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/"@en . "de-identified data"@en . . . . "A 'data protected' role between a user and given data entails that a user must be authorized in order to view that data."@en . "Damion Dooley" . "data protected"@en . . . _:genid223 . _:genid223 . _:genid223 "1"^^ . _:genid224 . _:genid225 . _:genid227 _:genid226 . _:genid225 _:genid227 . _:genid226 . _:genid226 . _:genid226 . _:genid227 . _:genid224 _:genid225 . _:genid223 _:genid224 . _:genid223 . _:genid228 . _:genid228 . _:genid228 "1"^^ . _:genid229 . _:genid230 . _:genid232 _:genid231 . _:genid230 _:genid232 . _:genid231 . _:genid231 . _:genid231 . _:genid232 . _:genid229 _:genid230 . _:genid228 _:genid229 . _:genid228 . . "A datum containing the name of persons or institute who collected a given specimen."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/"^^ . "specimen collector"@en . . . . "Damion Dooley" . "NCBI BioSample culture identifier"@en . . . "A user identifier is an identifier provided as part of an authentication process of a client (user) to a service (server). User identifiers normally persist over time, in contrast to session identifiers which are temporary."@en . "Damion Dooley" . "user identifier"@en . . . "sequence identifier"@en . . . "metagenomic species identification"@en . . . "Note: REPLACE WITH Citation: SIO_000174 ????"@en . "document citation identifier"@en . . . "organization identifier"@en . . . "collection identifier"@en . . . "variant calling / pathogen identification and clustering"@en . . . "isolate (pathogen) identification"@en . . "http://purl.obolibrary.org/obo/OBI_0001616"^^ . "obsolete: NCBI BioSample ID -"@en . "true"^^ . . . "1) Escherichia coli O104:H4 str. C227-11 clinical isolate 2010_333_NC-6\n2) CD8+ T cells from female TSG6-knockout BALB/c mouse\n3) Human metagenome isolated from urine of healthy female"@en . . "A specimen (or sample) title should be short and informative. Each specimen title must be unique in a submission."@en . "NCBI BioSample record documentation refers to a \"BioSample title\", stating that it is \"auto-generated if one is not supplied by the submitter.\" This is distinct from any assigned BioSession accession, or other \"external sample identifier\" that may have been issued by the source database or repository."@en . "Damion Dooley" . "specimen title"@en . . . "draft GenEpiO isolate source context"@en . . . "INSDC term (lower level)" . . "A categorical choice recorded when the data for a given measurable datum is available but not shared publicly because of information privacy concerns."@en . . . "restricted access"@en . . . "State (United States of America)"@en . . . _:genid233 . _:genid233 . _:genid234 . _:genid235 . _:genid237 _:genid236 . _:genid235 _:genid237 . _:genid236 . _:genid236 . _:genid236 . _:genid237 . _:genid234 _:genid235 . _:genid233 _:genid234 . _:genid233 . . "A health status trend is a short-term prognosis about whether health is improving, worsening or unchanging"@en . "Damion Dooley"@en . "health status trend datum"@en . . . "http://www.itis.gov" . . "The Integrated Taxonomic Information System (ITIS) contains authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world."@en . "Damion Dooley" . "Integrated Taxonomic Information System"@en . "ITIS" . "ITIS"@en . . . "https://www.nlm.nih.gov/mesh/meshhome.html"@en . . "MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity."@en . "Damion Dooley" . "Medical Subject Headings"@en . "MSH" . "MESH"@en . . . "https://ncit.nci.nih.gov/ncitbrowser/" . . "The National Cancer Institute Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities."@en . "Damion Dooley" . "National Cancer Institude Thesaurus"@en . "NCI_Thesaurus" . "NCIt" . "NCIT"@en . . . . "The NIFSTD ontology of the Neuroscience Information Framework is composed of a collection of OWL modules with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, organism, function and dysfunction."@en . "Damion Dooley" . "https://wiki.nci.nih.gov/display/VKC/NIFSTD+Ontology"^^ . "NIFSTD"@en . . . . "SNOMED CT is a large clinical health terminology product owned and distributed by SNOMED International."@en . "Damion Dooley" . "http://www.snomed.org/snomed-ct"^^ . "SNOMEDCT" . "SNOMEDCT"@en . . . "http://www.fao.org/fishery/collection/asfis/en" . . "ASFIS is a database curated by the United Nations Food And Agriculture Organization (FAO) Fisheries and Aquaculture Statistics and Information Branch (FIPS). It contains over 12,700 species items selected according to their interest or relation to fisheries and aquaculture."@en . "Damion Dooley" . "UN FAO Fisheries and Aquaculture Statistics and Information Branch database"@en . "FAO ASFIS" . "ASFIS"@en . . . . "FTT"@en . . . . "TGN"@en . . . . "Wikipedia is a free online encyclopedia that aims to allow anyone to edit articles."@en . "Damion Dooley"@en . "https://en.wikipedia.org/wiki/Wikipedia"^^ . "Wikipedia"@en . . . . "SWEETRealm"@en . . . . "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."@en . "Damion Dooley" . "http://www.geonames.org/"^^ . "Geonames"@en . . . "http://ecolexicon.ugr.es/en/index.htm" . . "EcoLexicon is a terminological resource developed by the LexiCon Research Group at the University of Granada."@en . "Damion Dooley" . "EcoLexicon"@en . . . . "A standard established for use by the Integrated Rapid Infectious Disease Analysis (IRIDA) project, which is a Canadian-led initiative to build an open source, end-to-end platform for infectious disease genomic epidemiology."@en . "Damion Dooley" . "http://www.irida.ca/"^^ . "draft IRIDA standard"@en . . . . "ISO 3166-1 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for the names of countries, dependent territories, and special areas of geographical interest."@en . "Damion Dooley" . "https://en.wikipedia.org/wiki/ISO_3166-2"^^ . "ISO3166-1"@en . . . . "ISO 3166-2 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for identifying the principal subdivisions (e.g., provinces or states) of all countries coded in ISO 3166-1."@en . "Damion Dooley" . "https://en.wikipedia.org/wiki/ISO_3166-1"^^ . "ISO3166-2"@en . . . . "Information Technology \u2013 Codes For The Identification Of The States And Equivalent Areas Within The United States, Puerto Rico, And The Insular Areas"@en . "Damion Dooley" . "American National Standards Institute"@en . "ANSI INCITS 38"@en . . . . "Damion Dooley" . "The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical."@en . "https://nhd.usgs.gov/gnis.html"^^ . "GNISID"@en . . . . "LTER"@en . . . _:genid238 . _:genid238 . _:genid238 . _:genid238 . "order:\nOBI:0001628 # investigation identifier\nOBI:0001616 # specimen identifier\nGENEPIO:0001808 # specimen title\nGENEPIO:0000113 # specimen category\nsep:00196 # specimen description\nOBI:0001479 # specimen from organism\nGENEPIO:0001640 # specimen organism taxonomy (species)\nGENEPIO:0000027 # specimen source context\nGENEPIO:0001722 # NCBI specimen voucher\nGENEPIO:0001429 # strain identifier \nGENEPIO:0001798 # NCBI BioSample culture identifier\nGENEPIO:0001717 # viral subtype\nOMP:0000207 # serotype phenotype\nSO:0001027 # genotype\nGENEPIO:0001079 # serovar\nGENEPIO:0001716 # subgroup\nGENEPIO:0001055 # NCBI pathotype\nGENEPIO:0001054 # isolate passage history\nGENEPIO:0001656 # latitude and longitude coordinate\nGENEPIO:0001657 # NCBI BioSample geo_loc_name model\nGENEPIO:0001051 # NCBI BioSample isolate (human name or description)\nGENEPIO:0001648 # NCBI Contributing organization / project\nGENEPIO:0001797 # specimen collector\nOBI:0001619 # specimen collection date\nOBI:0001888 # sequencing facility contact person\nGENEPIO:0001651 # INSDC institution code\nGENEPIO:0001721 # NCBI culture collection\nGENEPIO:0001567 # subject (host) taxonomic species\nGENEPIO:0001724 # subject organism common name\nGENEPIO:0001775 # subject age at time of specimen collection\nGENEPIO:0000026 # subject health status at time of specimen extraction\nGENEPIO:0000031 # subject sex\nGENEPIO:0001614 # subject description\nGENEPIO:0001617 # subject disease\nGENEPIO:0001625 # subject disease stage\nGENEPIO:0001212 # subject disease outcome" . . "A National Center for Biotechnology Information BioSample specification defines fields and terms that provide \"descriptions of biological source materials used in experimental assays\"."@en . "Damion Dooley"@en . "http://www.ncbi.nlm.nih.gov/biosample/"^^ . "NCBI BioSample Pathogen.cl standard"@en . "https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/"^^ . . . _:genid239 . _:genid239 . _:genid239 "1"^^ . _:genid240 . _:genid241 . _:genid243 _:genid242 . _:genid241 _:genid243 . _:genid242 . _:genid242 . _:genid242 . _:genid243 . _:genid240 _:genid241 . _:genid239 _:genid240 . _:genid239 . _:genid244 . _:genid244 . _:genid244 "1"^^ . _:genid244 . _:genid244 . _:genid245 . _:genid245 . _:genid245 "1"^^ . _:genid245 . _:genid245 . _:genid246 . _:genid246 . _:genid246 "1"^^ . _:genid247 . _:genid248 . _:genid250 _:genid249 . _:genid248 _:genid250 . _:genid249 . _:genid249 . _:genid249 . _:genid250 . _:genid247 _:genid248 . _:genid246 _:genid247 . _:genid246 . _:genid251 . _:genid251 . _:genid251 "1"^^ . _:genid252 . _:genid253 . _:genid255 _:genid254 . _:genid253 _:genid255 . _:genid254 . _:genid254 . _:genid254 . _:genid255 . _:genid252 _:genid253 . _:genid251 _:genid252 . _:genid251 . . "The National Center for Biotechnology Information BioProject standard is a collection of datums that describe biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project."@en . "Damion Dooley" . "http://www.ncbi.nlm.nih.gov/bioproject/"@en . "NCBI lists project data type and other controlled vocabulary fields at : https://www.ncbi.nlm.nih.gov/books/NBK54364/"@en . "NCBI BioProject standard"@en . _:genid256 . _:genid256 . _:genid256 . _:genid257 . _:genid257 . _:genid257 "1"^^ . _:genid258 . _:genid259 . _:genid261 _:genid260 . _:genid259 _:genid261 . _:genid260 . _:genid260 . _:genid260 . _:genid261 . _:genid258 _:genid259 . _:genid257 _:genid258 . _:genid256 _:genid257 . _:genid256 "Objective"@en . _:genid262 . _:genid262 . _:genid262 . _:genid263 . _:genid263 . _:genid263 "1"^^ . _:genid263 . _:genid262 _:genid263 . _:genid262 "The format of the BioProject Accession is five alpha-letters followed by one to six numbers. For example PRJNA43021"@en . _:genid262 "Project Accession"@en . _:genid264 . _:genid264 . _:genid264 . _:genid265 . _:genid265 . _:genid265 "1"^^ . _:genid266 . _:genid267 . _:genid269 _:genid268 . _:genid267 _:genid269 . _:genid268 . _:genid268 . _:genid268 . _:genid269 . _:genid266 _:genid267 . _:genid265 _:genid266 . _:genid264 _:genid265 . _:genid264 "Methodology"@en . . . "http://www.aha.org/content/00-10/overview0302.pdf"^^ . "http://www.webcitation.org/5VBWPbFgY"^^ . . "The American Hospital Association has issued HIPAA Updated Guidelines for Releasing Information on the Condition of Patients"@en . "Damion Dooley" . "American Hospital Association HIPAA Standard"@en . "AHA HIPPA" . "AHA HIPPA standard"@en . . . "http://www.ncbi.nlm.nih.gov/pubmed/"@en . . "PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites."@en . "NCBI PubMed"@en . "PMID" . "PubMed"@en . . . "http://www.pulsenetinternational.org/"@en . . "PulseNet, a national and international surveillance system used to identify and respond to foodborne disease outbreaks, has a standardized laboratory method and data submission standard for pathogen isolate typing test results and related isolate contextual data. From this information clusters of disease can be identified that might represent unrecognized outbreaks."@en . "Pulse Net International BioSample Metadata"@en . "PulseNet" . "PulseNet submission standard"@en . "https://www.cdc.gov/pulsenet/pathogens/index.html"^^ . "https://www.nml-lnm.gc.ca/Pulsenet/index-eng.htm"@en . . . . _:genid270 . _:genid270 . _:genid270 . _:genid270 . _:genid271 . _:genid271 . _:genid271 . _:genid271 . "AHA HIPPA: http://www.aha.org/content/00-10/overview0302.pdf" . . "Good - Vital signs are stable and within normal limits. Patient is conscious and comfortable. Indicators are excellent."@en . "Damion Dooley"@en . . . "AHA Hippa: Good"@en . "good health status"@en . _:genid272 . _:genid272 . _:genid272 . _:genid272 . _:genid272 "Good"@en . _:genid273 . _:genid273 . _:genid273 . _:genid273 . _:genid273 "satisfactory"@en . . . . _:genid274 . _:genid274 . _:genid274 . _:genid274 . _:genid275 . _:genid275 . _:genid275 . _:genid275 . . "Fair - Vital signs are stable and within normal limits. Patient is conscious, but may be uncomfortable. Indicators are favorable."@en . "Damion Dooley"@en . . "fair health status"@en . _:genid276 . _:genid276 . _:genid276 . _:genid276 . _:genid276 "fair"@en . _:genid277 . _:genid277 . _:genid277 . _:genid277 . _:genid277 "Stable"@en . . . . _:genid278 . _:genid278 . _:genid278 . _:genid278 . _:genid279 . _:genid279 . _:genid279 . _:genid279 . . "Serious - Vital signs may be unstable and not within normal limits. Patient is acutely ill. Indicators are questionable."@en . "Damion Dooley"@en . . "serious health status"@en . _:genid280 . _:genid280 . _:genid280 . _:genid280 . _:genid280 "Serious"@en . . . _:genid281 . _:genid281 . _:genid282 . _:genid283 . _:genid285 _:genid284 . _:genid283 _:genid285 . _:genid284 . _:genid284 . _:genid284 . _:genid285 . _:genid282 _:genid283 . _:genid281 _:genid282 . _:genid281 . . "A health status history datum is a record of the longer-term pattern or presence of a given patient's health status."@en . "Damion Dooley" . "health status history datum"@en . . "(0,0) is the origin of the cartesian coordinate system."@en . "\"In mathematics, the origin of a Euclidean space is a special point, usually denoted by the letter O, used as a fixed point of reference for the geometry of the surrounding space.\n\nIn physical problems, the choice of origin is often arbitrary, meaning any choice of origin will ultimately give the same answer. This allows one to pick an origin point that makes the mathematics as simple as possible, often by taking advantage of some kind of geometric symmetry.\""@en . "Damion Dooley"@en . "https://en.wikipedia.org/wiki/Origin_(mathematics)"^^ . "origin"@en . . . "https://en.wikipedia.org/wiki/Medical_state"@en . "United Kingdom National Health Service trusts, boards, etc. have some terminology in common for public disclosure of patient health conditions."@en . "Damion Dooley"@en . "National Health Service terminology"@en . "NHS standard"@en . . . . _:genid286 . _:genid286 . _:genid286 . _:genid286 . _:genid287 . _:genid287 . _:genid287 . _:genid287 . . "Damion Dooley" . "Damion Dooley's note: This is a contentious term. AHA calls for it never to be used, since the common phrase \"critical but stable\" is misleading by the very nature of \"critical\". The NHS however has it as one of its central terms. The use of \"stable\" also points to a health trend, rather than a state. A separate \"health status trend datum\" has been set up to capture this."@en . "critical but stable health status"@en . _:genid288 . _:genid288 . _:genid288 . _:genid288 . _:genid288 "critical but stable"@en . . . . _:genid289 . _:genid289 . _:genid289 . _:genid289 . _:genid290 . _:genid290 . _:genid290 . _:genid290 . "NHS Terms: https://en.wikipedia.org/wiki/Medical_state" . . "Damion Dooley" . "comfortable health status"@en . _:genid291 . _:genid291 . _:genid291 . _:genid291 . _:genid291 "Comfortable"@en . . . . _:genid292 . _:genid292 . _:genid292 . _:genid292 . _:genid293 . _:genid293 . _:genid293 . _:genid293 . . "Damion Dooley" . "progressing well health status"@en . _:genid294 . _:genid294 . _:genid294 . _:genid294 . _:genid294 "progressing well"@en . . . . . "Damion Dooley"@en . "Damion Dooley note: This term (weakly) implies that the patient is recovered enough to be released from hospital. Technically this isn't a health status though, it is a patient medical service state."@en . "discharged from hospital"@en . _:genid295 . _:genid295 . _:genid295 . _:genid295 . _:genid295 "discharged"@en . . . . "A data item which is about the collection state of a datum at some point in time."@en . "Damion Dooley note: We'll need to incorporate NIAID GSCID-BRC Sample data standards mention:\nUnknown/Not Applicable/Censored Allowed\nUnknown/not applicable/not available/ available upon request"@en . "Damion Dooley"@en . "A given datum's datum status value is metadata, i.e. a statement about a particular datum, often when no actual data entry or categorical choice for that datum has been made."@en . "datum status"@en . "INSDC missing value reporting terms:\nhttp://www.ebi.ac.uk/ena/about/missing-values-reporting"@en . . . . "A categorical choice indicating that a datum is available for retrieval."@en . "Damion Dooley"@en . "In theory any datum that has a recorded value has 'recorded' for its datum status."@en . "recorded"@en . . . . . "Patient is awaiting physician and/or assessment."@en . "Very similar to 'datum status' 'in process' status."@en . "Damion Dooley"@en . . "undetermined health status - awaiting assessment"@en . . . _:genid296 . _:genid296 . _:genid296 . _:genid296 . . "Damion Dooley" . "deteriorating"@en . "worsening health trend"@en . . . "This covers the description of data and abstract structure in n-dimensional space. Within space there are coordinate systems, coordinates, and entities made up of coordinates."@en . "Damion Dooley"@en . . _:genid297 . _:genid297 . _:genid297 . _:genid297 . "/^[N+](:\\d(\\.\\d+)?)$/, $lat\n/^S(:\\d(\\.\\d+)?)$/, '-' + $lat"^^ . "/^(:[-S+N])?(:[1-8]?[0-9](:\\.\\d{1,6})?)$/, $lat$degree.$decimal\n/^(:[-S+N])?(:90(:\\.0{1,6})?))$/, $lat$degree.$decimal"^^ . "/^(\\d(\\.\\d+)?)$/, '+\\1'"^^ . . "A decimal latitude measurement in degrees in conformance with the ISO 6709 standard."@en . "This is failing Hermit reasoner since it rejects totalDigits, and fractionDigits: \n'has primitive data type' exactly 1 xsd:decimal[>= -90.0 , <= 90.0 , totalDigits 8 , fractionDigits 6]'"@en . "Damion Dooley" . . _:genid298 . _:genid298 . _:genid298 . _:genid298 . "/^(:[-W+E])?(:(1[0-7]|[1-9])?[0-9])(:\\.\\d{1,6})?)$/, $long$degree.$decimal\n/^(:[-W+E])?(:180(:\\.0{1,6})?)$,$long$degree.$decimal"^^ . . "A decimal longitude measurement in degrees in conformance with the ISO 6709 standard."@en . "Damion Dooley" . . "Damion Dooley" . . "A 2D coordinate system is a coordinate system in 2 dimensional space. Each coordinate is composed of an offset from the origin of each dimension"@en . "Damion Dooley" . . "Damion Dooley" . . "Damion Dooley" . . _:genid299 . _:genid299 . _:genid299 . _:genid299 . _:genid300 . _:genid300 . _:genid300 . _:genid300 . "A datetime range intermediate datum is a datetime item grouped under a process, and occuring after some process start and before some process end."@en . "Damion Dooley" . "datetime range intermediate"@en . . "Damion Dooley" . "datetime range item"@en . . _:genid301 . _:genid301 . _:genid301 . _:genid301 . "The ending date of a process"@en . "datetime range end"@en . . _:genid302 . _:genid302 . _:genid302 . _:genid302 . "Damion Dooley" . "The starting date of a process"@en . "datetime range start"@en . . "Damion Dooley" . _:genid303 . _:genid303 . _:genid303 . _:genid303 . . "Damion Dooley" . . . "A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a named river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time."@en . "Damion Dooley" . . . "A Canadian postal code is a postal code that pertains to a geographic region of Canada."@en . "Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account."@en . . "A \"USA zip code\" is a five digit (Zone Improvement Plan) or 9 digit postal code pertaining to a region of the United States of America. The optional trailing 4 digits of a 9 digit zip code provide greater granularity of delivery target."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/NCIT_C25720" . "obsolete: US postal code"@en . "true"^^ . . . . "Damion Dooley" . "entity history record"@en . . . . "Damion Dooley" . "generic range history record"@en . . . . "Damion Dooley"@en . "A set does not have a direct distance metric between its members."@en . . . "Damion Dooley" . . "Damion Dooley" . . . "Damion Dooley" . _:genid304 . _:genid304 . _:genid304 . _:genid304 . _:genid305 . _:genid305 . _:genid305 . _:genid305 . _:genid306 . _:genid306 . _:genid306 . _:genid306 . _:genid307 . _:genid307 . _:genid307 . _:genid307 . _:genid308 . _:genid308 . _:genid308 . _:genid308 . _:genid309 . _:genid309 . _:genid309 . _:genid309 . . "Damion Dooley" . . . . "A product name and model number of a manufacturer's genomic (dna) sequencer."@en . "Damion Dooley" . "sequencing instrument model"@en . . . . . _:genid310 . _:genid310 . _:genid310 "1"^^ . _:genid310 . _:genid310 . _:genid311 . _:genid311 . _:genid311 "1"^^ . _:genid311 . _:genid311 . . "A circle is a simple closed shape in Euclidean geometry. It is the set of all points in a plane that are at a given distance from a given point, the centre; equivalently it is the curve traced out by a point that moves so that its distance from a given point is constant."@en . "Damion Dooley" . "https://en.wikipedia.org/wiki/Circle"^^ . "circle"@en . . . "NCBI SRA: ILLUMINA" . "Illumina platform"@en . . . "NCBI SRA: COMPLETE_GENOMICS" . "Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: \"Complete Genomics\u2019 sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs\u2122). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL\u2122). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010).\"" . "Complete Genomics platform"@en . . . _:genid312 . _:genid312 . _:genid312 "0"^^ . _:genid312 . _:genid312 . _:genid313 . _:genid313 . _:genid313 "1"^^ . _:genid313 . _:genid313 . . "Damion Dooley" . "earth area boundary census"@en . . . "NCBI SRA: LS454" . "Roche LS454 platform"@en . . . "NCBI SRA: PACBIO_SMRT" . "PacBio platform"@en . . . "NCBI SRA: AB SOLiD 4hq" . "SOLiD 4hq System"@en . . . "NCBI SRA: AB SOLiD 5500" . "SOLiD 5500"@en . . . "NCBI SRA: AB SOLiD 5500xl" . "SOLiD 5500xl"@en . . . "NCBI SRA: AB SOLiD PI System" . "SOLiD PI System"@en . . . "NCBI SRA: AB SOLiD System 2.0" . "SOLiD System 2.0"@en . . . "NCBI SRA: AB SOLiD System 3.0" . "SOLiD System 3.0"@en . . . . "A two dimensional entity is an entity composed of one or more points on a two dimensional surface."@en . "Damion Dooley"@en . "2D entity"@en . . "NCBI SRA: Ion Torrent PGM" . . . "NCBI SRA: 454 GS FLX Titanium" . "454 Genome Sequencer FLX Titanium"@en . . . . "NCBI SRA: 454 GS" . "454 Genome Sequencer"@en . . . "NCBI SRA: 454 GS Junior" . "454 Genome Sequencer Junior"@en . . . . "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly" . "Whether any method was used to select for or against, enrich, or screen the material being sequenced."@en . "Damion Dooley" . "NCBI SRA: LIBRARY_SELECTION" . "library selection"@en . . . "Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C)."@en . "NCBI SRA: 5-methylcytidine antibody" . "5-methylcytidine antibody method"@en . . . "Cap-analysis gene expression."@en . "NCBI SRA: CAGE" . "CAGE method"@en . . . "Cot-filtered highly repetitive genomic DNA"@en . "NCBI SRA: CF-H" . "CF-H method"@en . . . "Cot-filtered moderately repetitive genomic DNA"@en . "NCBI SRA: CF-M" . "CF-M method"@en . . . "Cot-filtered single/low-copy genomic DNA"@en . "NCBI SRA: CF-S" . "CF-S method"@en . . . "Cot-filtered theoretical single-copy genomic DNA"@en . "NCBI SRA: CF-T" . "CF-T method"@en . . . "Chromatin immunoprecipitation"@en . "NCBI SRA: ChIP" . "ChIP method"@en . . . "Deoxyribonuclease (MNase) digestion"@en . "NCBI SRA: DNAse" . "DNAse method"@en . . . "Hypo-methylated partial restriction digest"@en . "NCBI SRA: HMPR" . "HMPR method"@en . . . "Selection by hybridization in array or solution."@en . "NCBI SRA: Hybrid Selection" . "Hybrid Selection method"@en . . . "Enrichment by methyl-CpG binding domain."@en . "NCBI SRA: MBD2 protein methyl-CpG binding domain" . "MBD2 protein methyl-CpG binding domain method"@en . . . "Methyl Filtrated"@en . "NCBI SRA: MF" . "MF method"@en . . . "Micrococcal Nuclease (MNase) digestion"@en . "NCBI SRA: MNase" . "MNase method"@en . . . "Methylation Spanning Linking Library"@en . "NCBI SRA: MSLL" . "MSLL method"@en . . . "Source material was selected by designed primers."@en . "NCBI SRA: PCR" . "PCR method"@en . . . "Rapid Amplification of cDNA Ends."@en . "NCBI SRA: RACE" . "RACE method"@en . . . "Source material was selected by randomly generated primers."@en . "NCBI SRA: RANDOM PCR" . "RANDOM PCR method"@en . . . "Random selection by shearing or other method."@en . "NCBI SRA: RANDOM" . "RANDOM method"@en . . . "Source material was selected by reverse transcription PCR"@en . "NCBI SRA: RT-PCR" . "RT-PCR method"@en . . . "Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling."@en . "NCBI SRA: Reduced Representation" . "Reduced Representation method"@en . . . "DNA fractionation using restriction enzymes."@en . "NCBI SRA: Restriction Digest" . "Restriction Digest method"@en . . . "PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA."@en . "NCBI SRA: cDNA" . "cDNA method"@en . . . "Physical selection of size appropriate targets."@en . "NCBI SRA: size fractionation" . "size fractionation method"@en . . . "Other library enrichment, screening, or selection process."@en . "NCBI SRA: other" . "other library method"@en . . . "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly" . "The library source specifies the type of source material that is being sequenced."@en . "Damion Dooley" . "library source"@en . . . "Genomic DNA (includes PCR products from genomic DNA)."@en . "Damion Dooley" . "NCBI SRA: GENOMIC" . "genomic source"@en . . . "Mixed material from metagenome."@en . "Damion Dooley"@en . "NCBI SRA: METAGENOMIC" . "metagenomic source"@en . . . "Transcription products from community targets"@en . "Damion Dooley" . "NCBI SRA: METATRANSCRIPTOMIC" . "metatranscriptomic source"@en . . . "Other, unspecified, or unknown library source material."@en . "Damion Dooley" . "NCBI SRA: OTHER" . "other library source"@en . . . "Synthetic DNA."@en . "Damion Dooley" . "NCBI SRA: SYNTHETIC" . "synthetic source"@en . . . "Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries)."@en . "Damion Dooley" . "NCBI SRA: TRANSCRIPTOMIC" . "transcriptomic source"@en . . . "Viral RNA."@en . "Damion Dooley" . "NCBI SRA: VIRAL RNA" . "viral RNA source"@en . . . "Sequencing technique intended for this library."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly" . "library strategy"@en . . . "Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA"@en . "NCBI SRA: AMPLICON" . "amplicon strategy"@en . . . "MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status."@en . "NCBI SRA: Bisulfite-Seq" . "Bisulfite-Seq strategy"@en . . . "Clone end (5', 3', or both) sequencing."@en . "NCBI SRA: CLONEEND" . "clone end strategy"@en . . . "Genomic clone based (hierarchical) sequencing."@en . "NCBI SRA: CLONE" . "clone strategy"@en . . . "Concatenated Tag Sequencing"@en . "NCBI SRA: CTS" . "CTS strategy"@en . . . "Direct sequencing of chromatin immunoprecipitates."@en . "NCBI SRA: ChIP-Seq" . "ChIP-Seq strategy"@en . . . "Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI."@en . "NCBI SRA: DNase-Hypersensitivity" . "DNase-Hypersensitivity strategy"@en . . . "Single pass sequencing of cDNA templates"@en . "NCBI SRA: EST" . "EST strategy"@en . . . "Sequencing intended to finish (close) gaps in existing coverage."@en . "NCBI SRA: FINISHING" . "finishing strategy"@en . . . "Full-length sequencing of cDNA templates"@en . "NCBI SRA: FL-cDNA" . "FL-cDNA strategy"@en . . . "Direct sequencing of methylated fractions sequencing strategy."@en . "NCBI SRA: MBD-Seq" . "MBD-Seq strategy"@en . . . "Direct sequencing following MNase digestion."@en . "NCBI SRA: MNase-Seq" . "MNase-Seq strategy"@en . . . "Methylation-Sensitive Restriction Enzyme Sequencing strategy."@en . "NCBI SRA: MRE-Seq" . "MRE-Seq strategy"@en . . . "Methylated DNA Immunoprecipitation Sequencing strategy."@en . "NCBI SRA: MeDIP-Seq" . "MeDIP-Seq strategy"@en . . . "Library strategy not listed."@en . "NCBI SRA: OTHER" . "other library strategy"@en . . . "Shotgun of pooled clones (usually BACs and Fosmids)."@en . "NCBI SRA: POOLCLONE" . "pool clone strategy"@en . . . "Random sequencing of whole transcriptome."@en . "NCBI SRA: RNA-Seq" . "RNA-Seq strategy"@en . . . "Random sequencing of a whole chromosome or other replicon isolated from a genome."@en . "NCBI SRA: WCS" . "WCS strategy"@en . . . "Random sequencing of the whole genome."@en . "NCBI SRA: WGS" . "WGS strategy"@en . . . "Random sequencing of exonic regions selected from the genome."@en . "NCBI SRA: WXS" . "WXS strategy"@en . . . "Free form text describing the protocol by which the sequencing library was constructed."@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly"@en . "library construction protocol"@en . . . . "The submitter's name for this library."@en . "Damion Dooley" . "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly"@en . "NCBI SRA: LIBRARY_NAME"@en . "library name"@en . . . . "A two dimensional boundary is a continuous path (loop) defined on a two dimensional surface."@en . "Damion Dooley"@en . "2D boundary"@en . . . "cfu/100mL"@en . . "A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid."@en . "Should this be deprecated? Need to find working examples that actually use / 100mL."@en . "Damion Dooley" . "colony forming unit per 100 milliliter"@en . . . . "A multiplier in the decimal number system that has been applied to an accompanying number or set of numbers often to simplfy their appearance. Numbers described by multipliers may have lost significant digits through rounding or trimming."@en . "Damion Dooley" . "decimal quantity unit"@en . . . . "draft tuberculosis - dataset features and provenance"@en . . . . "draft tuberculosis - case specimen characteristics"@en . . . . "draft tuberculosis - case subject characteristics"@en . . . . "draft tuberculosis - case risk factors"@en . . . . "draft tuberculosis - case clinical presentation"@en . . . . "draft tuberculosis - case laboratory testing"@en . . . . "draft tuberculosis - case medication"@en . . . . "draft isolate whole genome sequencing model"@en . . . . "draft tuberculosis - case model"@en . . . . "A Mycobacterium tuberculosis lineage is a named family of strains of tuberculosis, named usually with reference to their shared geographic origin."@en . "Damion Dooley" . "Mycobacterium tuberculosis lineage"@en . "A TB-Lineage identification tool using spoligotypes and MIRU data:\nhttp://tbinsight.cs.rpi.edu/run_tb_lineage.html"^^ . "Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans\nhttp://www.nature.com/ng/journal/v45/n10/full/ng.2744.html"^^ . . . "TB lineage 2 - East-Asian, includes Bejing"@en . . . "TB lineage 3 - East-African Indian, includes CAS/Delhi"@en . . . "TB lineage 4 - Euro-American, includes Haarlem, LAM3, X, T, F11, H37Rv"@en . . . "TB lineage 1 - Indo-Oceanic"@en . . . "TB lineage 5 - West African 1"@en . . . "TB lineage 6 - West African 2"@en . . . . "Damion Dooley"@en . "An isolate preparation facility is a type of organization that provides the service of isolating organisms of interest from provided specimens."@en . "isolate preparation facility"@en . . . "plant product"@en . . . _:genid314 . _:genid314 . _:genid314 . _:genid314 . "geospatial name"@en . . . . "A personal health datum is a datum that pertains to the health situation or history of an individual."@en . "Personal health datum covers the following information\n\n'has member' some 'analytic datum'\n'has member' some 'behavioural risk factor'\n'has member' some 'country of birth'\n'has member' some 'dietary restrictions'\n'has member' some 'Disease Attributes'\n'has member' some 'health status history datum'\n'has member' some 'health status trend datum'\n'has member' some 'host hospital service status'\n'has member' some 'subject disease stage'\n'has member' some 'subject health status'\n'has member' some 'subject health status (AHA)'\n'has member' some 'subject health status (GSCID-BRC)'\n'has member' some 'subject health status (NCIT)'\n'has member' some 'subject health status (UK NHS)'\n'has member' some 'subject health status at time of specimen extraction'\n'has member' some 'tuberculosis disease anatomical site'\n'has member' some comorbidity\n'has member' some disease\n'has member' some symptom" . "Damion Dooley"@en . "personal health datum"@en . . . "A host hospital service status indicates the state of a host's interaction with hospital medical services."@en . "Damion Dooley"@en . "host hospital service status"@en . . . . "Damion Dooley"@en . "admitted to hospital"@en . . . . "Received treatment but not admitted."@en . . "treated and released (not admitted to hospital)"@en . _:genid315 . _:genid315 . _:genid315 . _:genid315 . _:genid315 "Treated and Released"@en . . . . "Received treatment. Transferred to a different facility."@en . . "treated and transferred"@en . _:genid316 . _:genid316 . _:genid316 . _:genid316 . _:genid316 "Treated and Transferred"@en . . . . _:genid317 . _:genid317 . _:genid317 . _:genid317 . _:genid318 . _:genid318 . _:genid318 . _:genid318 . . "Damion Dooley" . "satisfactory health status"@en . _:genid319 . _:genid319 . _:genid319 . _:genid319 . _:genid319 "satisfactory"@en . . . "depth:1" . "subject health status (UK NHS)"@en . . . "depth:1" . "subject health status (AHA)"@en . "http://purl.obolibrary.org/obo/GENEPIO_0002019"@en . . . _:genid320 . _:genid320 . _:genid320 . _:genid320 . _:genid321 . _:genid321 . _:genid321 . _:genid321 . "stable health trend"@en . "http://purl.obolibrary.org/obo/GENEPIO_0001669"@en . . "An ordinal variable is a categorical variable whose values have sequential order, but no distance metric between them."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/STATO_0000228"^^ . "obsolete: ordinal variable"@en . "true"^^ . . . "mapping (reference based)"@en . . . "data protection item"@en . . . "subject provided consent"@en . . . . "Damion Dooley" . "An ordinal tree specification is a value specification entity whose subclasses each represent a possible value selection, and which have a linear order with respect to their siblings."@en . "ordinal value specification"@en . . . "consent datum"@en . . . "agency provided consent"@en . . . . "2019-11-17T00:43:00Z"^^ . "draft ISO sequence repository field"@en . . . "Centre of circle, ellipse or parabola; centre of mass."@en . . "A centre point is a point used in the description of an n-dimentional entity from which other (given) aspects of the entity are most efficienty described. A point of symmetry. The entity must have only one such point."@en . "Probably a better formal math defn?"@en . "Damion Dooley" . "centre point"@en . . . . "This covers the following entities:\n\n'has member' some 'antimicrobial phenotype'\n'has member' some 'antimicrobial resistance test drug'\n'has member' some 'antimicrobial resistance test platform'\n'has member' some 'antimicrobial resistance testing method'\n'has member' some 'antimicrobial resistance testing method version or reagent'\n'has member' some 'antimicrobial resistance testing reference standard'\n'has member' some 'antimicrobial resistance testing reference standard version'\n'has member' some 'antimicrobial resistance tissue specificity'\n'has member' some 'antimicrobial resistant plasmid type'\n'has member' some 'automated testing platform vendor'\n'has member' some 'draft antibiogram drug test model'\n'has member' some 'in-vitro microbial susceptibility test'\n'has member' some 'measurement comparator'\n'has member' some 'MIC unit'\n'has member' some 'MIC value'\n'has member' some 'Minimum Inhibitory Concentration Test'\n'has member' some 'test drug maximum concentration'\n'has member' some 'test drug minimum concentration'\n'has member' some 'tuberculosis treatment drug'" . "Damion Dooley"@en . "This is a collection of antibiotic resistance process parameters and outputs"@en . "phenotypic antimicrobial drug susceptibility test datum"@en . . "The resistance phenotype of an isolate represents the interpretation of an MIC value with regard to some breakpoint threshold e.g. resistant (R), sensitive (S), intermediate (I), wild type (WT), or non-wild type (NWT)"@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/NCIT_C85539" . "obsolete: antimicrobial resistance phenotype"@en . "true"^^ . . "Intermediate resistance indicates that an isolate is observed to offer an intermediate level of resistance to a given antibiotic."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/NCIT_C85560" . "obsolete: antibiotic intermediate resistance (I)"@en . "true"^^ . . "Non-susceptible indicates that an isolate is observed to offer complete resistance to a given antibiotic."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/NCIT_C85561" . "obsolete: antibiotic nonsensitive (high resistance)"@en . "true"^^ . . . . "A not defined resistance indicates that an isolate was not tested against a given antibiotic, or the result of the test was inconclusive."@en . "Damion Dooley note: Is this the same as \"indeterminate\"?"@en . "Damion Dooley" . "N" . "ND" . "antibiotic resistance not defined"@en . . "Resistant indicates that an isolate is observed to offer a greater than intermediate level of resistance to a given antibiotic."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/NCIT_C85562" . "obsolete: antibiotic resistant (R)"@en . "true"^^ . . "Susceptible indicates that an isolate is observed to offer a detectable but less than intermediate level of resistance to a given antibiotic."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/NCIT_C85563" . "obsolete: antibiotic sensitive (S)"@en . "true"^^ . . "Susceptible - dose dependent indicates that an isolate is observed to offer resistance to a given antibiotic when a sufficient dose is given."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/NCIT_C85559" . "obsolete: sensitive - dose dependent"@en . "true"^^ . . . _:genid322 . _:genid322 . _:genid322 . _:genid322 . . "A MIC test measurement resulting from a laboratory dilution method."@en . "Damion Dooley's note: is this still useful? Currently \"MIC dilution measurement specification' refers directly via 'is about' to \"broth dilution method\" but that may be too specific."@en . "Damion Dooley" . "MIC dilution measurement datum"@en . . "The type of assay used to determine the minimum inhibitory concentration."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/NCIT_C85540" . "obsolete: antimicrobial resistance testing method"@en . "true"^^ . . . "http://purl.obolibrary.org/obo/NCIT_C85555"^^ . "obsolete: agar dilution evidence"@en . "true"^^ . . . . "The commercial kit or product used to determine the MIC e.g. E-Test. If a commercial product was not used, include the type of media used."@en . "Damion Dooley"@en . "antimicrobial resistance testing method device or reagent"@en . . . . ""@en . "antimicrobial resistant plasmid type"@en . . "The instrumentation used to determine minimum inhibitory concentration values."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/ARO_3004390"^^ . "obsolete: antimicrobial resistance testing platform"@en . "true"^^ . . "http://purl.obolibrary.org/obo/ARO_3004400"^^ . "obsolete: Microscan"@en . "true"^^ . . "http://purl.obolibrary.org/obo/ARO_3004401"^^ . "obsolete: Phoenix"@en . "true"^^ . . "http://purl.obolibrary.org/obo/ARO_3004402"^^ . "obsolete: Sensititre"@en . "true"^^ . . "http://purl.obolibrary.org/obo/ARO_3004403"^^ . "obsolete: Vitek"@en . "true"^^ . . "http://purl.obolibrary.org/obo/ARO_3004409"^^ . "obsolete: Trek"@en . "true"^^ . . . "obsolete: manual - noncommercial"@en . "true"^^ . . "The manufacturer of an antibiotic resistance lab typing platform"@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/ARO_3004404"^^ . "obsolete: antimicrobial resistance testing platform vendor"@en . "true"^^ . . "http://purl.obolibrary.org/obo/ARO_3004407"^^ . "obsolete: Siemens"@en . "true"^^ . . "http://purl.obolibrary.org/obo/ARO_3004406"^^ . "obsolete: Biom\u00E9rieux"@en . "true"^^ . . "http://purl.obolibrary.org/obo/ARO_3004405"^^ . "obsolete: Becton Dickinson"@en . "true"^^ . . . . "A manual in vitro diagnostic device used by laboratories to determine the MIC (Minimum Inhibitory Concentration) and whether or not a specific strain of bacterium or fungus is susceptible to the action of a specific antimicrobial."@en . "Damion Dooley"@en . . "E-Test"@en . "Epsilometer test"@en . "Etest (device)"@en . . . . "GM-NEG"@en . . "The clinical and laboratory guidelines or standards that prescribe the threshold values for determining resistance phenotypes."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/ARO_3004360"^^ . "obsolete: antimicrobial resistance testing reference standard"@en . "true"^^ . . "BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership"@en . "Damion Dooley" . . "BSAC"^^ . "obsolete: British Society for Antimicrobial Chemotherapy (BSAC)"@en . "true"^^ . . "The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards"@en . "Damion Dooley" . "NCCLS"@en . "http://clsi.org"^^ . . "CLSI" . "On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI"@en . "obsolete: Clinical and Laboratory Standards Institute (CLSI)"@en . "true"^^ . . "DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations."@de . "Damion Dooley" . "http://www.din.de/en/din-and-our-partners/din-e-v"^^ . . "DIN"^^ . "Deutsches Institut f\u00FCr Normung"@de . "obsolete: German Institute for Standardization (DIN)"@en . "true"^^ . . "EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in vitro antimicrobial susceptibility testing."@en . "Damion Dooley" . "http://www.eucast.org/"^^ . . "EUCAST"^^ . "obsolete: European Committe on Antimicrobial Susceptibility Testing (EUCAST)"@en . "true"^^ . . "Damion Dooley" . . "NCCLS"^^ . "obsolete: National Committee on Clinical Laboratory Standards (NCCLS)"@en . "true"^^ . . "La SFM a vocation \u00E0 rassembler les microbiologistes de France et des pays francophones, travaillant dans les diff\u00E9rents domaines de la microbiologie m\u00E9dicale, industrielle, et environnementale, en physiologie, g\u00E9n\u00E9tique, taxonomie, hygi\u00E8ne, agents antimicrobiens, ...concernant les bact\u00E9ries, virus, champignons et parasites."@fr . "The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents."@en . "This isn't at moment considered a valid EBI antibiogram choice?" . "Damion Dooley" . "http://www.sfm-microbiologie.org/"^^ . . "SFM"^^ . "obsolete: Soci\u00E9t\u00E9 Fran\u00E7aise de Microbiologie (SFM)" . "true"^^ . . . . "Damion Dooley" . "SIR"^^ . "SIR"@en . . . . "Damion Dooley" . "WRG"^^ . "WRG"@en . . . "first line tuberculosis drug"@en . . . "last resort antibiotic"@en . . . "NIAID standard"@en . . "NIAID provides The GSCID/BRC Project and Sample Application Standard. It is designed to capture standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases."@en . "Damion Dooley" . "https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards"^^ . "National Institute of Allergy and Infectious Disease standard"@en . . . "A RefSeq accession identifier is an accession identifier for selected NCBI-curated genomic, transcript and protein sequences. These identifiers are distinct from DDBJ/EMBL/GenBank identifiers."@en . "Damion Dooley"@en . "RefSeq accession identifier"@en . "http://www.ncbi.nlm.nih.gov/refseq/about/" . . . "A Genomic Standards Consortium standard is an international, community-driven standard to facilitate genomic data integration, discovery and comparison."@en . "Damion Dooley"@en . "Genomic Standards Consortium (GSC) standard"@en . "http://gensc.org/"^^ . . . . "A landform, biome or built environment at site that a given specimen was collected from."@en . "Damion Dooley"@en . "specimen collection site - geographic feature"@en . . . _:genid323 . _:genid323 . _:genid323 . _:genid323 . "A particular human patient, or a given animal or plant."@en . . "An investigative subject which is an organism."@en . "Damion Dooley"@en . "subject organism"@en . . . . "help=The number of passages should be expressed as a numerical value."@en . . "The number of serial iterations that an isolate is grown in one environment."@en . "Damion Dooley"@en . "number of passages"@en . . . . "help:The passage protocol should include, when applicable, inoculum size, media type, temperature and duration of incubation."@en . "A passage protocol should detail the number of serial iterations that an isolate is grown in one environment, and the conditions of that environment."@en . "Damion Dooley"@en . "passage protocol"@en . . "The unit provided for an antibiotic drug test dosage."@en . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/ARO_3004372"^^ . "obsolete: drug minimum inhibitory concentration unit"@en . "true"^^ . . . "order:\nGENEPIO:0001237 # specimen type (host or environmental context)\nOBI:0001619 # specimen collection date\nOBI:0000659 # specimen collection process\nGENEPIO:0002094 # specimen collection device\nGENEPIO:00001600 # draft sequence repository data - geographic location\nENVO:00010483 # environmental material\nENVO:00002297 # environmental feature\nGENEPIO:0001567 # subject (host) taxonomic species\nGENEPIO:0000110 # subject health status\nGENEPIO:0001617 # subject disease\nGENEPIO:0000028 # subject body product\nGENEPIO:0000025 # specimen source anatomical site\nFOODON:03411564 # draft sequence repository data - food processing" . . "draft sequence repository data - specimen collection"@en . . . "order:\nGENEPIO:0002105 # Specimen processing organization role\nNCIT:C93874 # organization name\nNCIT:C40974 # first name\nNCIT:C40975 # last name\nNCIT:C93582 # job title\nNCIT:C42775 # email address\nGENEPIO:0001756 # phone\nNCIT:C25464 # Country\nENVO:00000005 # major administrative subdivision -> GAZ state/province/territory/region)\nNCIT:C80234 # Municipality\u201D (via GenEpiO -> GAZ cities)\nNCIT:C25690 # Street Address" . . "Contact information for an organization related to specimen collection, processing or storage."@en . "Damion Dooley"@en . "contact specification - specimen related organization"@en . . . "dateFormat:ISO 8601" . "order:\nGENEPIO:0002082 # specimen related organization\nGENEPIO:0002081 # specimen collection\nGENEPIO:0002086 # geographic location\nGENEPIO:0002084 # isolate\nGENEPIO:0002087 # isolate history\nGENEPIO:0002106 # food specimen\nGENEPIO:0002088 # antibiogram\nGENEPIO:0002085 # sequencing\nGENEPIO:0002090 # sequencing QC\nGENEPIO:0002089 # virulence\nGENEPIO:0002092 # submission to EBI\nGENEPIO:0002091 # submission to NCBI/DDBJ" . . "This draft specification provides a collection of fields related to the contextual data of a specimen, its genomic sequencing, and its pathogenic epidemiology."@en . "Damion Dooley"@en . "draft sequence repository contextual data standard"@en . . . "order:\nGENEPIO:0001640 # specimen taxonomy\nGENEPIO:0001429 # strain identifier\nGENEPIO:0001644 # isolate identifier\nOBI:0000079 # culture medium\nGENEPIO:0002107 # isolation medium" . . "draft sequence repository data - isolate"@en . . . "order:\n\nGENEPIO:0000069 # sequencing date\nOBI:0000079 # culture medium\u201D (via MicrO, yields a list of formulas).\nGENEPIO:0002093 # sequencing dna extraction method\nEFO:0000683 # replicate\nGENEPIO:0000085 # library preparation kit\nGENEPIO:0000149 # library preparation kit version\nGENEPIO:0000075 # sequencing chemistry\nGENEPIO:0001921 # sequencing instrument model\nGENEPIO:0000150 # read trimming and filtering software\nGENEPIO:0000084 # read adapter trimming software\nGENEPIO:0002095 # read paired-end merging software\nGENEPIO:0000090 # assembly method\nGENEPIO:0000151 # bioinformatics pipeline name\nGENEPIO:0000153 # bioinformatics pipeline protocol\nGENEPIO:0000152 # bioinformatics pipeline version\nGENEPIO:0000095 # genome annotation algorithm" . . "draft sequence repository data - sequencing"@en . . . "order:\nGENEPIO_0001656 # latitude and longitude ISO 6709\nGENEPIO:0000118 # specimen collection country\nGENEPIO:0002097 # specimen collection state/prov/ter/region\nGENEPIO:0001785 # specimen collection city" . . "The geographical origin of the sample by city, region, country or latitude and logitude."@en . "Damion Dooley"@en . "draft sequence repository data - geographic location"@en . . . "order:\nGENEPIO:0002078 # number of passages\nGENEPIO:0002079 # passage protocol" . . "draft sequence repository data - isolate passage history"@en . . . "order:\nGENEPIO:0001100 # antimicrobial drug tests\nGENEPIO:0002101 # test drug minimum concentration\nGENEPIO:0002100 # test drug maximum concentration\nGENEPIO:0002045 # antimicrobial resistance testing method\nGENEPIO:0002047 # antimicrobial testing method version or reagent\nGENEPIO:0002062 # antimicrobial resistance testing reference standard\nGENEPIO:0002049 # antimicrobial resistance testing platform"@en . . "A dataset of the minimal inhibitory concentrations (value, unit, sign (<,>, =)) and resistance phenotypes (resistant, sensitive or undetermined) of the sequenced isolate against different antibiotics tested."@en . "Damion Dooley"@en . "draft sequence repository data - antibiogram"@en . . . "order:\nGENEPIO:0002130 # Virulence factor name\nGENEPIO:0002131 # Virulence testing protocol\nGENEPIO:0002132 # detection limit" . . "The virulence factors determined to be present in the sequenced isolate by phenotypic or target amplification methods e.g. Shiga toxins, hemolysins."@en . "Damion Dooley"@en . "draft sequence repository data - virulence"@en . . . "order:\nOBI:0001941 # N50\nGENEPIO_0000092 # sequencing depth / read coverage" . . "Measurements or calculated quantities used to assess the extent and success of the sequence assembly process. Metric thresholds are species-specific."@en . "Damion Dooley"@en . "draft sequence repository data - sequencing quality control"@en . . . "order:\nOBI:0001616 # specimen identifier\nGENEPIO:0001644 # isolate identifier\nGENEPIO:0001429 # strain identifier\nGENEPIO:0001640 # specimen organism taxonomy\nGENEPIO:0000113 # specimen category\nOBI:0001619 # specimen collection date\nGENEPIO:0001797 # specimen collector\nGENEPIO:0001657 # geo_loc_name\nGENEPIO:0001656 # latitude and longitude coord\nGENEPIO:0000027 # specimen source context\nGENEPIO:0001567 # subject organism taxonomy\nGENEPIO:0001724 # subject organism common name\nGENEPIO:0001617 # subject disease" . . ""@en . "Damion Dooley"@en . "draft sequence repository data - submission to NCBI/DDBJ"@en . . . "order:\nGENEPIO:0001644 # isolate identifier\nGENEPIO:0001429 # strain identifier\nGENEPIO:0001640 # specimen organism taxonomy\nGENEPIO:0001079 # serovar \nGENEPIO:0002135 # EBI environmental feature\nGENEPIO:0000113 # specimen category\nOBI:0001619 # specimen collection date\nGENEPIO:0001797 # specimen collector\nGENEPIO:0002086 # geographic location\nGENEPIO:0000027 # specimen source context\nGENEPIO:0002076 # geographic feature\nGENEPIO:0001567 # subject taxonomy\nGENEPIO:0000110 # subject health status"@en . . ""@en . "Damion Dooley"@en . "draft sequence repository data - submission to EBI"@en . "https://www.ebi.ac.uk/ena/submit/pathogen-data"@en . . . . "The procedure used to obtain genomic DNA from a sample through chemical, physical or mechanical means."@en . "Damion Dooley"@en . "sequencing dna extraction method datum"@en . . . "The tool or device used to extract a specimen."@en . "Damion Dooley"@en . "specimen collection device"@en . . . "The name and version of the software used to merge paired-end reads before assembly."@en . "read paired-end merging software"@en . . . "Sequencing" . "The name and version of the software product used for removal of adapter sequences from demultiplexed data reads"@en . "GROUP: IRIDA Ontology (Emma)" . "GENEPIO" . "read adapter trimming software"@en . . . _:genid324 . _:genid324 . _:genid325 . _:genid326 . _:genid327 . _:genid326 _:genid327 . _:genid328 . _:genid327 _:genid328 . _:genid329 . _:genid328 _:genid329 . _:genid329 . _:genid325 _:genid326 . _:genid324 _:genid325 . _:genid324 . . "An ontology identifier or textual name of the most precise geographical location available for the site of a specimen collection event."@en . "Damion Dooley" . "Adapted from NIAID GSCID-BRC metadata working group"@en . "Note that this is expressed in a particular format in some standards."@en . "specimen collection location - state/province/territory/region"@en . _:genid330 . _:genid330 . _:genid330 . _:genid331 . _:genid331 . _:genid332 . _:genid333 . _:genid334 . _:genid333 _:genid334 . _:genid335 . _:genid334 _:genid335 . _:genid336 . _:genid335 _:genid336 . _:genid336 . _:genid332 _:genid333 . _:genid331 _:genid332 . _:genid330 _:genid331 . _:genid330 "lookup" . . "A wild type (WT) resistance phenotype indicates a bacterial pathogen belongs to a \"Na\u00EFve\", susceptible wild-type population with respect to a given antimicrobial. No acquired or mutational resistance mechanisms are\npresent to the antimicrobial in question."@en . "Damion Dooley"@en . "https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf"@en . "http://purl.obolibrary.org/obo/ARO_3004432"^^ . "obsolete: wild type (WT)"@en . "true"^^ . . "A non-wild type (WT) resistance phenotype indicates a bacterial pathogen has an acquired or mutational resistance mechanism present with respect to the antimicrobial in question. The bacteria has a reduced susceptibility to this agent."@en . "Damion Dooley"@en . "https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf"@en . "http://purl.obolibrary.org/obo/ARO_3004433"^^ . "obsolete: non-wild type (NWT)"@en . "true"^^ . . . . "This is the maximum concentration of a drug applied during an an assay."@en . "Damion Dooley"@en . "test drug maximum concentration"@en . . . . "This is the minimum concentration of a drug applied during an an assay."@en . "Damion Dooley"@en . "test drug minimum concentration"@en . . "The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results."@en . "Damion Dooley" . "http://purl.obolibrary.org/obo/ARO_3004430"^^ . "obsolete: antimicrobial resistance tissue specificity"@en . "true"^^ . . . "depth:1" . "order:\nNCIT:C115935 # healthy\nNCIT:C126054 # non-pathalogical\nNCIT:C25610 # pathologic\nNCIT:C82508 # life threatening\nNCIT:C28554 # deceased"@en . "subject health status (NCIT)"@en . . . "order:\nNCIT:C40974 # first name\nNCIT:C40975 # last name\nNCIT:C93582 # job title\nNCIT:C42775 # email address\nGENEPIO:0001756 # phone" . "contact specification - professional role"@en . . . . "An organization related to the collection, isolate production, sequencing or storage of specimen material or data."@en . "Damion Dooley"@en . "specimen processing organization type"@en . . . "order:\nGENEPIO:0001533 # food specimen type\nFOODON:03450002 # food cooking method\nFOODON:03440011 # extent of heat treatment\nFOODON:03430113 # physical state, shape or form\nFOODON:03470107 # food preservation method\nFOODON:03490100 # container or wrapping\nFOODON:03480020 # food packing medium\nFOODON:03500010 # food contact surface\nGENEPIO:0000139 # food cultural origin\nFOODON:03460111 # treatment applied to food" . "This specification offers food source, product type, packaging and processing attributes relevant to describing a food specimen."@en . "draft sequence repository data - food specimen"@en . . . . "An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment."@en . "Chris has proposed this term for OBI as \"enrichment culture medium\""@en . "Damion Dooley"@en . "isolation medium"@en . . . "order:\nGENEPIO:0000121 # start date\nGENEPIO:0000122 # end date\nGENEPIO:0001783 # travel destination\nGENEPIO:0001064 # travel mode\nGENEPIO:0001065 # travel reason" . . "This record details a person's travel movement and duration for epidemiological analysis."@en . "Damion Dooley"@en . "draft travel log specification"@en . . . "order:\nOBI:0001616 # BioSample_ID\nGENEPIO:0001640 # Species\nGENEPIO:0001187 # Antibiotic_Name\nGENEPIO:0002062 # AST_Standard\nGENEPIO:0002111 # Breakpoint_version\nNCIT:C85540 # Laboratory_typing_method\nGENEPIO:0002112 # Measurement\nGENEPIO:0002080 # Measurement_units\nGENEPIO:0001001 # Measurement_sign\nNCIT:C85539 # Resistance_phenotype\nGENEPIO:0002181 # Resistance_phenotype - ECOFF\nGENEPIO:0002049 # Platform" . . "A standard for European Bioinformatics Institute (EBI) antibiogram data submission"@en . "Damion Dooley"@en . "draft EBI antimicrobial susceptibility test V. 2017-08-30"@en . "https://github.com/EBI-COMMUNITY/compare-amr/blob/master/Antimicrobial-susceptibility-testing-data-submission_V_2017-08-30.pdf"@en . . . _:genid337 . _:genid337 . _:genid337 . _:genid337 . . "A MIC test measurement resulting from a laboratory diffusion method."@en . "Damion Dooley's note: is this still useful? Currently \"MIC diffusion measurement specification' refers directly via 'is about' to \"Disk Diffusion Method\"."@en . "Damion Dooley"@en . "MIC diffusion measurement datum"@en . . . . "The version of the antimicrobial reistance testing reference standard protocol used in assessing an isolate."@en . "Damion Dooley" . "antimicrobial resistance testing reference standard version"@en . . . "This is a component of an antibiogram that enables a choice of MIC measurements based on either the diffusion or dilution method. These methods call for different numeric input ranges and units."@en . "draft sequence repository data - antibiogram MIC measurement"@en . . . _:genid338 . _:genid338 . _:genid338 "1"^^ . _:genid338 . _:genid338 . _:genid339 . _:genid339 . _:genid339 . _:genid339 . "time value specification"@en . . . . "The process of collecting a portion of feces from an organism."@en . "Emma Griffiths"@en . "stool collection"@en . "feces collection"@en . . . . "The process of collecting a portion of urine from an organism."@en . "Emma Griffiths"@en . "sputum collection"@en . . . . "The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids."@en . "Emma Griffiths"@en . "rinsing for specimen collection"@en . . . . "The process of collecting specimen material using a swab collection device."@en . "Emma Griffiths"@en . "swabbing for specimen collection"@en . . . . "The process of collecting bodily fluids that have been discharged from blood vessels usually arising from inflammation or injury."@en . "Emma Griffiths"@en . "exudate collection"@en . . . . "The removal or collection of specimen material through the use of suction."@en . "Emma Griffiths"@en . "vacuuming for specimen collection"@en . . . . "Emma Griffiths"@en . "NOTE: there are different types of tubes with coloured caps indicating different preservatives etc."@en . "tube containing media or preservative"@en . . . "Emma Griffiths"@en . "NOTE: there are different types of tubes with coloured caps indicating different preservatives etc."@en . "tube containing antimicrobial"@en . . . . "Emma Griffiths"@en . "Whirlpak sampling bag"@en . . . . "Emma Griffiths"@en . "spoon"@en . . . . "Emma Griffiths"@en . "fork"@en . . . . "Emma Griffiths"@en . "hand scoop"@en . . . "Emma Griffiths"@en . "trier"@en . . . . "Emma Griffiths"@en . "vaccum device"@en . . . _:genid340 . _:genid340 . _:genid340 . _:genid340 . "investigation identifier specification"@en . . . "order:\nGENEPIO:0001640 # taxonomy\nGENEPIO:0002086 # geographic location\nGENEPIO:0002076 # geographic feature\nGENEPIO:0002106 # food\nFOODON:03510136 # food consumer\nGENEPIO:0002094 # specimen collection device\nGENEPIO:0000025 # anatomical site\nGENEPIO:0000028 # body product\nGENEPIO:0001724 # host organism common name\nGENEPIO:0001567 # host taxonomy\nUBERON:0000105 # life cycle\nGENEPIO:0001639 # antigenic formula\nGENEPIO:0001718 # serotype specification\nGENEPIO:0000045 # PFGE test specification" . . "This is a draft (under development) collection of fields for capturing the contextual data for Enterobase (https://enterobase.warwick.ac.uk/) records."@en . "Damion Dooley"@en . "draft Enterobase contextual data standard"@en . . . _:genid341 . _:genid341 . _:genid341 . _:genid341 . . "The name of the virulence factor molecule produced by a pathogen that specifically causes disease, or that influences the host's function to allow the pathogen to thrive."@en . "Emma Griffiths"@en . "virulence factor name"@en . . . _:genid342 . _:genid342 . _:genid342 . _:genid342 . "help:The protocol for determining virulence should include, when applicable, inoculum preparation, platforms and instrumentation, conditions, cell lines and animal models."@en . . "The laboratory protocol used to determine virulence phenotypes and markers."@en . "Emma Griffiths"@en . "virulence testing protocol name"@en . . . _:genid343 . _:genid343 . _:genid343 . _:genid343 . "help:Detection limits should include the numerical cut-off (threshold) value and units for determining positive results e.g. qPCR value, CFUs."@en . "The detection limit denotes the smallest measure that can be detected with reasonable certainty for a given analytical procedure."@en . "Emma Griffiths"@en . "detection limit"@en . . . . "A disease cluster is an unusually high incidence of a particular disease or disorder occurring in close proximity in terms of both time and geography."@en . "Damion Dooley"@en . "https://en.wikipedia.org/wiki/Disease_cluster"@en . "disease cluster"@en . . . . . "A disease cluster in which two or more cases have been linked by an infectious disease transmission process."@en . "Damion Dooley"@en . "infectious disease cluster"@en . . . "help:used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. entries including /environmental_sample must not include the /strain qualifier"@en . "Identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism. Environmental samples include clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host. They do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture)."@en . "ENA Webin:environmental_feature"@en . "EBI ENA Webin environmental feature"@en . . . . "The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Webin is an ENA interface and standard for sequence submissions."@en . "https://www.ebi.ac.uk/ena"@en . "EBI European Nucleotide Archive Webin"@en . "https://www.ebi.ac.uk/ena/WebFeat/"@en . . . "help:Breadth of coverage should be reported as a percentage value (e.g. 95%) to a fold of coverage (e.g. 10X)."@en . . "The breadth of coverage is the percentage of the genome that was sequenced to a prescribed depth of coverage."@en . "Emma Griffiths"@en . "breadth of coverage"@en . . . . "The mean contig length is the count of base pairs in the average size contig of the sequence assembly."@en . "Emma Griffiths"@en . "mean contig length"@en . . . "order:\nGENEPIO:0000084 # read adapter trimming (y/n)\nGENEPIO:0002096 # read adapter trimming software\nGENEPIO:0002095 # read paired-end merging software\nGENEPIO:0000150 # read trimming and filtering software" . . "The procedures used to remove adapters from raw sequence reads, trim low quality bases and where applicable, merge paired-end reads."@en . "Emma Griffiths"@en . "raw sequence data processing datum"@en . . . . "Name of strain from which sample was obtained OR name of isolate from which sample was obtained."@en . "Damion Dooley"@en . "specimen strain or isolate identifier"@en . . . _:genid344 . _:genid344 . _:genid345 . _:genid345 . _:genid347 _:genid346 . _:genid346 "\\s*(\\d(.\\d{1,4})?|[1-8]\\d(.\\d{1,4})?|90(.0{1,4})?)\\s*[WEwe]\\s*(\\d(.\\d{1,4})?|[1-9]\\d(.\\d{1,4})?|1[0-7]\\d(.\\d{1,4})?|180(.0{1,4})?)\\s*[NSns]\\s*" . _:genid347 . _:genid345 _:genid347 . _:genid344 _:genid345 . _:genid344 . . "The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format \"d[d.dddd] N|S d[dd.dddd] W|E\", eg, 38.98 N 77.11 W"@en . "Damion Dooley"@en . "https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/"@en . "latitude and longitude coordinate (NCBI BioSample format)"@en . . . _:genid348 . _:genid348 . _:genid348 . _:genid348 . "decimal value specification"@en . . . _:genid349 . _:genid349 . _:genid349 . _:genid349 . "floating point value specification"@en . . . _:genid350 . _:genid350 . _:genid350 . _:genid350 . "unsigned integer"@en . "A 32 bit number having a range 0 - 4294967295."@en . "unsigned integer value specification"@en . . . _:genid351 . _:genid351 . _:genid351 "1"^^ . _:genid352 . _:genid353 . _:genid354 . _:genid353 _:genid354 . _:genid355 . _:genid354 _:genid355 . _:genid356 . _:genid355 _:genid356 . _:genid356 . _:genid352 _:genid353 . _:genid351 _:genid352 . _:genid351 . _:genid357 . _:genid357 . _:genid357 "1"^^ . _:genid357 . _:genid357 . _:genid358 . _:genid358 . _:genid358 . _:genid358 . "date value specification"@en . . . _:genid359 . _:genid359 . _:genid359 . _:genid359 . _:genid360 . _:genid360 . _:genid360 "1"^^ . _:genid361 . _:genid362 . _:genid363 . _:genid362 _:genid363 . _:genid364 . _:genid363 _:genid364 . _:genid364 . _:genid361 _:genid362 . _:genid360 _:genid361 . _:genid360 . "A specification for the size of an assembled genome as measured in base pairs."@en . "This is a decimal because the megabasepair unit may involve a fractional component."@en . "assembly genome size specification"@en . . . _:genid365 . _:genid365 . _:genid365 . _:genid365 . "sequencing facility name specification"@en . . . "date (ISO 8601)"@en . "A date should be recorded as YYYY-MM-DD according to ISO 8601. HOWEVER ... OWL 2.0 does not include xsd:date as a permitted data type, so this value specification only accepts xsd:dateTime"@en . "date value specification (ISO 8601)"@en . . . _:genid366 . _:genid366 . _:genid366 . _:genid366 . "strain identifier specification"@en . . . _:genid367 . _:genid367 . _:genid367 . _:genid367 . _:genid368 . _:genid368 . _:genid368 . _:genid368 . _:genid369 . _:genid369 . _:genid369 "1"^^ . _:genid369 . _:genid369 . _:genid370 . _:genid370 . _:genid371 . _:genid371 . _:genid373 _:genid372 . _:genid372 "5"^^ . _:genid375 _:genid374 . _:genid373 _:genid375 . _:genid374 "100"^^ . _:genid375 . _:genid371 _:genid373 . _:genid370 _:genid371 . _:genid370 . "A MIC test measurement resulting from a laboratory diffusion method."@en . "Damion Dooley"@en . "MIC diffusion measurement specification"@en . . . _:genid376 . _:genid376 . _:genid376 . _:genid376 . "unsigned short"@en . "A 16 bit integer ranging from 0 - 65535"@en . "unsigned short integer value specification"@en . . . _:genid377 . _:genid377 . _:genid377 "1"^^ . _:genid378 . _:genid379 . _:genid380 . _:genid379 _:genid380 . _:genid380 . _:genid378 _:genid379 . _:genid377 _:genid378 . _:genid377 . "genomic sequence length specification"@en . . . _:genid381 . _:genid381 . _:genid381 . _:genid381 . _:genid382 . _:genid382 . _:genid382 . _:genid382 . _:genid383 . _:genid383 . _:genid383 "1"^^ . _:genid384 . _:genid385 . _:genid386 . _:genid385 _:genid386 . _:genid386 . _:genid384 _:genid385 . _:genid383 _:genid384 . _:genid383 . _:genid387 . _:genid387 . _:genid388 . _:genid388 . _:genid390 _:genid389 . _:genid389 "0.01"^^ . _:genid392 _:genid391 . _:genid390 _:genid392 . _:genid391 "2048.0"^^ . _:genid392 . _:genid388 _:genid390 . _:genid387 _:genid388 . _:genid387 . "A MIC test measurement resulting from a laboratory dilution method."@en . "Damion Dooley" . "MIC dilution measurement specification"@en . . . _:genid393 . _:genid393 . _:genid393 . _:genid393 . "The date on which a specimen was collected, in ISO 8601 format."@en . "specimen collection date (ISO 8601)"@en . . . _:genid394 . _:genid394 . _:genid394 . _:genid394 . "date of diagnosis (ISO 8601)"@en . . . _:genid395 . _:genid395 . _:genid395 . _:genid395 . _:genid396 . _:genid396 . _:genid396 . _:genid396 . _:genid397 . _:genid397 . _:genid397 "1"^^ . _:genid398 . _:genid399 . _:genid400 . _:genid399 _:genid400 . _:genid401 . _:genid400 _:genid401 . _:genid402 . _:genid401 _:genid402 . _:genid402 . _:genid398 _:genid399 . _:genid397 _:genid398 . _:genid397 . _:genid403 . _:genid403 . _:genid404 . _:genid404 . _:genid406 _:genid405 . _:genid405 "0"^^ . _:genid406 . _:genid404 _:genid406 . _:genid403 _:genid404 . _:genid403 . "A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time."@en . "Damion Dooley"@en . "subject age specification"@en . . . _:genid407 . _:genid407 . _:genid407 . _:genid407 . "subject age at time of specimen collection specification"@en . . . _:genid408 . _:genid408 . _:genid408 . _:genid408 . _:genid409 . _:genid409 . _:genid409 "1"^^ . _:genid409 . _:genid409 . "boolean"@en . . "A boolean value specification indicates a presence (true value) or absence (false value) of a given feature." . "Damion Dooley"@en . "boolean value specification"@en . . . _:genid410 . _:genid410 . _:genid410 . _:genid410 . "specimen identifier specification"@en . . . _:genid411 . _:genid411 . _:genid411 . _:genid411 . _:genid412 . _:genid412 . _:genid413 . _:genid413 . _:genid415 _:genid414 . _:genid414 "[A-Za-z0-9]+([_.\\-][A-Za-z0-9]+)*\\@[A-Za-z0-9]+([.\\-][A-Za-z0-9]+){1,3}" . _:genid415 . _:genid413 _:genid415 . _:genid412 _:genid413 . _:genid412 . "email address specification"@en . . . _:genid416 . _:genid416 . _:genid417 . _:genid418 . _:genid419 . _:genid418 _:genid419 . _:genid420 . _:genid419 _:genid420 . _:genid421 . _:genid420 _:genid421 . _:genid421 . _:genid417 _:genid418 . _:genid416 _:genid417 . _:genid416 . "region, province, state or territory specification"@en . . . _:genid422 . _:genid422 . _:genid422 . _:genid422 . "A specification for a geographic location that a specimen was collected at."@en . "specimen collection site specification"@en . . . _:genid423 . _:genid423 . _:genid423 . _:genid423 . "subject organism common name specification"@en . . . _:genid424 . _:genid424 . _:genid424 . _:genid424 . "A subject identifier specification is a specification including datatype pertaining to a given standard's subject identifier field."@en . "Damion Dooley"@en . "subject identifier specification"@en . . . _:genid425 . _:genid425 . _:genid425 . _:genid425 . _:genid426 . _:genid426 . _:genid426 . _:genid426 . "Name of disease in a subject that is related to a given investigation, study and/or specimen."@en . "Damion Dooley"@en . "NIAID GSCID-BRC metadata working group"@en . "Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID\nor https://www.ncbi.nlm.nih.gov/mesh/1000067"@en . "subject disease specification"@en . . . _:genid427 . _:genid427 . _:genid427 . _:genid427 . "unsigned long integer"@en . "A 64 bit integer ranging from 0 - 18446744073709551615"@en . "unsigned long integer value specification"@en . . . _:genid428 . _:genid429 . _:genid430 . _:genid429 _:genid430 . _:genid431 . _:genid430 _:genid431 . _:genid431 . _:genid428 _:genid429 . _:genid428 . . "The physical location that a specimen was collected at. The location may be described by geographic coordinates, city or other geopolitical entity, biome, etc."@en . "Damion Dooley"@en . "specimen collection site"@en . . . . _:genid432 . _:genid432 . _:genid432 . _:genid432 . "The unit provided for an antibiotic drug test dosage."@en . "Damion Dooley"@en . "drug MIC unit specification"@en . . . _:genid433 . _:genid433 . _:genid434 . _:genid435 . _:genid436 . _:genid435 _:genid436 . _:genid436 . _:genid434 _:genid435 . _:genid433 _:genid434 . _:genid433 . _:genid437 . _:genid437 . _:genid437 . _:genid437 . "Damion Dooley"@en . "A datum specification for the maximum concentration of a drug applied during an an assay."@en . "test drug maximum concentration specification"@en . . . _:genid438 . _:genid438 . _:genid439 . _:genid440 . _:genid441 . _:genid440 _:genid441 . _:genid441 . _:genid439 _:genid440 . _:genid438 _:genid439 . _:genid438 . _:genid442 . _:genid442 . _:genid442 . _:genid442 . "This is the minimum concentration of a drug applied during an an assay."@en . "Damion Dooley"@en . "test drug minimum concentration specification"@en . . . _:genid443 . _:genid443 . _:genid443 . _:genid443 . _:genid444 . _:genid444 . _:genid445 . _:genid445 . _:genid447 _:genid446 . _:genid446 "(1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7)" . _:genid447 . _:genid445 _:genid447 . _:genid444 _:genid445 . _:genid444 . "listeria antigen specification"@en . . . _:genid448 . _:genid448 . _:genid448 . _:genid448 . _:genid449 . _:genid449 . _:genid449 "1"^^ . _:genid450 . _:genid450 . _:genid452 _:genid451 . _:genid451 "url" . _:genid452 . _:genid450 _:genid452 . _:genid449 _:genid450 . _:genid449 . "URL specification"@en . . . _:genid453 . _:genid453 . _:genid453 . _:genid453 . _:genid454 . _:genid454 . _:genid455 . _:genid456 . _:genid457 . _:genid456 _:genid457 . _:genid457 . _:genid455 _:genid456 . _:genid454 _:genid455 . _:genid454 . "A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip."@en . "Damion Dooley" . "travel destination specification"@en . . . _:genid458 . _:genid458 . _:genid458 . _:genid458 . "A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted."@en . "Damion Dooley"@en . "specimen source substance specification"@en . . . _:genid459 . _:genid459 . _:genid459 . _:genid459 . "Damion Dooley note: OBI has a variety of subclasses like \"blood specimen\" and \"colon specimen\" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic \"derives from some [uberon term]\". GenEpiO takes a different approach in describing this class with lists for \"subject anatomical site\", \"subject body product\", and \"plant anatomy\"."@en . "specimen from organism specification"@en . . . _:genid460 . _:genid460 . _:genid460 "1"^^ . _:genid460 . _:genid460 . _:genid461 . _:genid461 . _:genid462 . _:genid462 . _:genid464 _:genid463 . _:genid463 "0"^^ . _:genid464 . _:genid462 _:genid464 . _:genid461 _:genid462 . _:genid461 . "duration specification"@en . . . "A field specification is the specification of a data field used in a data standard or database table. This includes at least a database field name, and optionally display name, description, and data type (binary blob, numeric, categorical, textual or cross-reference)."@en . "Damion Dooley"^^ . . "2019-04-17T23:04:53Z"^^ . "obsolete: field specification"@en . "true"^^ . . "Damion Dooley"@en . "http://purl.obolibrary.org/obo/ARO_3004431"^^ . "obsolete: antimicrobial resistance phenotype - epidemiological cut-off values"@en . "true"^^ . . . "Damion Dooley"^^ . "2019-04-17T23:41:35Z"^^ . "PulseNet Canada field"@en . . . "Damion Dooley"^^ . "2019-04-17T23:41:56Z"^^ . "PulseNet Canada Salmonella field"@en . . . "Damion Dooley"^^ . "2019-05-03T02:44:38Z"^^ . "specimen collection service"@en . . . "Damion Dooley"^^ . "2019-05-03T02:49:24Z"^^ . "bioinformatics analysis service"@en . . . "An isolate preparation service prepares isolates for molecular sequencing."@en . "Damion Dooley"^^ . "2019-05-03T02:51:51Z"^^ . . "isolate preparation service"@en . . . "order:\nGENEPIO:0002222 # specimen collection service\nGENEPIO:0002226 # specimen repository/biobank service\nGENEPIO:0002224 # isolate preparation service\nOBI:0001904 # sequencing service\nOBI:0000992 # DNA sequencing service\nGENEPIO:0002223 # bioinformatics analysis service"@en . "Damion Dooley"^^ . "2019-05-03T02:52:19Z"^^ . "specimen related service"@en . . . "Damion Dooley"^^ . "2019-05-03T03:24:33Z"^^ . "specimen repository/biobank service"@en . . . . . _:genid465 . _:genid465 . _:genid465 . _:genid465 . . "Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable."@en . . "2019-11-19T22:17:43Z"^^ . "grave"@en . "critical health status"@en . _:genid466 . _:genid466 . _:genid466 . _:genid466 . _:genid466 "critical"@en . _:genid467 . _:genid467 . _:genid467 . _:genid467 . _:genid467 "critical"@en . . . "A datum indicating one of six defined subspecies of Salmonella."@en . . . "2019-11-25T08:45:41Z"^^ . "Salmonella subspecies"@en . . . . "A PFGE pattern resulting from DNA fragmentation induced by the Spel enzyme."@en . . "2019-11-25T09:07:26Z"^^ . "PFGE Spel pattern"@en . . . . "A collection of organisms that is indicative of faecal\ncontamination."@en . . . "2020-02-08T20:15:43Z"^^ . "Fecal indicator organism collections include bacterial groups such as thermotolerant coliforms or E. coli. Hence, they only infer that pathogens may be present"@en . "fecal indicator"@en . . _:genid468 . _:genid469 . _:genid470 . _:genid469 _:genid470 . _:genid470 . _:genid468 _:genid469 . _:genid468 . . . "An isolate derived from a food sample."@en . "Damion Dooley"^^ . "2019-06-28T23:41:26Z"^^ . "food isolate"@en . . . . "A method for typing The RNA component of the small (30S) subunit of prokaryotic ribosomes."@en . . "2020-04-24T19:06:05Z"^^ . "microbial 16S RNA typing"@en . . . _:genid471 . _:genid471 . _:genid471 . _:genid471 . _:genid472 . _:genid472 . _:genid473 . _:genid473 . _:genid475 _:genid474 . _:genid474 "h(1|2|3|4|5|6|7|8|9|10|11|12|14|15|16|17|18|19|21|23|24|26|27|28|29|30|31|32|33|34|35|36|37|38|39|40|41|42|43|44|45|46|47|48|49|51|52|53|54|55|56)" . _:genid475 . _:genid473 _:genid475 . _:genid472 _:genid473 . _:genid472 . "E. coli H antigen specification"@en . . . _:genid476 . _:genid476 . _:genid476 . _:genid476 . _:genid477 . _:genid477 . _:genid478 . _:genid478 . _:genid480 _:genid479 . _:genid479 "O([1-9][0-9][0-9])" . _:genid480 . _:genid478 _:genid480 . _:genid477 _:genid478 . _:genid477 . "E. coli O antigen specification"@en . . . _:genid481 . _:genid481 . _:genid481 "1"^^ . _:genid481 . _:genid481 . "string"@en . "string value specification"@en . . . "A sequencing platform brand provided by Helicos corporation (now defunct)."@en . . "2020-04-24T22:50:49Z"^^ . "Helicos platform"@en . . . "A sequencing platform provided by the Ion Torrent company."@en . . "2020-04-24T22:54:06Z"^^ . "Ion Torrent platform"@en . . . "A sequencing platform provided by Life Technologies Corporation"@en . . "Sequencing by Oligonucleotide Ligation and Detection"@en . "2020-04-24T22:55:31Z"^^ . "SOLiD sequening platform"@en . . . "obsolete: drag swab"@en . "true"^^ . . _:genid482 . _:genid482 . _:genid482 . _:genid482 . . . "Rinse is the liquid output of rinsing plant, animal or other material with liquid with the objective of extracting specimen material from that liquid."@en . "Damion Dooley"^^ . "2019-06-28T20:07:25Z"^^ . "rinse"@en . . _:genid483 . _:genid484 . _:genid485 . _:genid484 _:genid485 . _:genid485 . _:genid483 _:genid484 . _:genid483 . . "Animal rinse is a rinse derived from animal material of one or more animals."@en . "Damion Dooley"^^ . "2019-06-28T20:11:45Z"^^ . "animal rinse"@en . . . "obsolete: surface wipe"@en . "true"^^ . . . _:genid486 . _:genid486 . _:genid486 . _:genid486 . _:genid487 . _:genid487 . _:genid487 . _:genid487 . "requires discussion"@en . "A personal health datum which specifies host health complications at time of specimen collection."@en . "0000-0002-9578-0788" . "2022-01-31T23:52:14Z"^^ . "host health complications at time of specimen collection" . . . _:genid488 . _:genid488 . _:genid488 . _:genid488 . _:genid489 . _:genid489 . _:genid489 . _:genid489 . "requires discussion"@en . "A personal health datum which specifies host pre-existing conditions and risk factors at time of specimen collection."@en . "0000-0002-9578-0788" . "2022-01-31T23:52:41Z"^^ . "pre-existing conditions and risk factors at time of specimen collection" . . . _:genid490 . _:genid490 . _:genid490 . _:genid490 . _:genid491 . _:genid491 . _:genid491 . _:genid491 . "requires discussion"@en . "A personal health datum which specifies host signs and symptoms at time of specimen collection."@en . "0000-0002-9578-0788" . "2022-01-31T23:53:13Z"^^ . "signs and symptoms at time of specimen collection" . . . . . . . _:genid492 . _:genid492 . _:genid492 . _:genid492 . _:genid493 . _:genid493 . _:genid493 "1"^^ . _:genid493 . _:genid493 . . . . . "symptom"@en . "http://purl.obolibrary.org/obo/SYMP_0000462" . . . "position of phenotype abnormality"@en . . . . . "http://www.ebi.ac.uk/efo/EFO_0001444"^^ . "Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards"@en . "Damion notes: Subclasses can actually have two components - the identifier, and the agency it is associated with. \n\nUnder the general concept of \"postal code\" one can place particular national postal code systems like the US Postal code."@en . . . . "2020-04-24T22:38:17Z"^^ . "pregnant woman"@en . . _:genid494 . _:genid495 . _:genid497 _:genid496 . _:genid495 _:genid497 . _:genid496 . _:genid496 . _:genid496 . _:genid499 _:genid498 . _:genid497 _:genid499 . _:genid498 . _:genid498 . _:genid498 . _:genid499 . _:genid494 _:genid495 . _:genid494 . . _:genid500 . _:genid501 . _:genid503 _:genid502 . _:genid501 _:genid503 . _:genid502 . _:genid502 . _:genid502 . _:genid503 . _:genid500 _:genid501 . _:genid500 . . . . . _:genid504 . _:genid505 . _:genid507 _:genid506 . _:genid505 _:genid507 . _:genid506 . _:genid506 . _:genid506 . _:genid507 . _:genid504 _:genid505 . _:genid504 . . . . . "http://www.ontobee.org/ontology/MI" . "data source"@en . . "Database that originally provided the interaction record for exchange purposes."@en . "PMID:14755292" . "Damion Dooley's note: GenEpiO is using members of this class for the first part of the hasDbXref relation. This is where we are keeping the mapping between a code and its source database.\n\nDepending on its context, hasDbXref annotations may point directly to metadata field names in the target database, and may be annotated with additional information that guides any additional specifications that impact on data conversion of these fields."@en . "source database"@en . . . "tissue collection (necropsy)"@en . "A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. [database_cross_reference: Merriam-Webster:Merriam-Websters_Online_Dictionary--11th_Ed]"@en . "necropsy"@en . . . "The Archaea constitute a domain and kingdom of single-celled microorganisms"@en . "Damion Dooley"@en . "https://en.wikipedia.org/wiki/Archaea"^^ . _:genid508 . _:genid508 . _:genid508 . _:genid508 . . . . . . . "subspecies"@en . . . . . . . . . . "Damion Dooley's note: this term was mistakenly placed in a list of GenEpiO diagnostic tests; in fact it references a material entity"@en . . . . . . . . . . . . . _:genid509 . _:genid509 . _:genid509 . _:genid509 . "healthy"@en . . . . . _:genid510 . _:genid510 . _:genid510 . _:genid510 . . . . . . . . . "NCIT offers this alternate definition which GenEpiO intends: \n\"A measurement that specifies the minimum concentration of the agent at which organism growth was inhibited.\""@en . "MIC" . "Clinical and Laboratory Standards Institute MIC antimicrobial testing standards at http://em100.edaptivedocs.info/GetDoc.aspx?doc=CLSI%20M100%20S27:2017&scope=user"@en . . . . . . . . . . . . . . . . . . . . . . . . . . . . . "A portion of an absorbent material attached to one end of a small stick for the purpose of applying or collecting material."@en . . "Emma Griffiths"@en . . . . . . . . . . . . . . . . . . . . "http://purl.obolibrary.org/obo/GEO_000000396"^^ . . . . . "diseased"@en . "sick"@en . . . . . . "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" . . . . . . . . . _:genid511 . _:genid513 _:genid512 . _:genid512 . _:genid512 . _:genid514 . _:genid515 . _:genid517 _:genid516 . _:genid515 _:genid517 . _:genid516 . _:genid516 . _:genid516 . _:genid517 . _:genid514 _:genid515 . _:genid512 _:genid514 . _:genid519 _:genid518 . _:genid513 _:genid519 . _:genid518 . _:genid518 . _:genid518 . _:genid519 . _:genid511 _:genid513 . _:genid511 . _:genid520 . _:genid520 . _:genid521 . _:genid521 . _:genid523 _:genid522 . _:genid522 "[A-Za-z0-9]+([_.\\-][A-Za-z0-9]+)*\\@[A-Za-z0-9]+([.\\-][A-Za-z0-9]+){1,3}" . _:genid523 . _:genid521 _:genid523 . _:genid520 _:genid521 . _:genid520 . "/^(:\\d{5}(-\\d{4})?)/, $zip" . . . . . . . . . . . . . . . . . _:genid524 . _:genid524 . _:genid524 . _:genid524 . . "deceased"@en . _:genid525 . _:genid525 . _:genid525 . _:genid525 . _:genid525 "deceased"@en . . . . . . . "phone"@en . . . . . . . . "A hollow cylinder, especially one for holding or conveying liquids."@en . "Damion Dooley"@en . . . . . . "Damion Dooley's note: It can also be used as an authorization token in some identification processes."@en . . . . . . . . . . . . . . . . . . . "Damion Dooley's note: here \"sample\" means more than one specimen merged together."@en . "pooled"@en . . . . . . . . . . . . . . . . . . . . . . . . . _:genid526 . _:genid526 . _:genid526 . _:genid526 . . "Damion Dooley" . . . . "Damion Dooley" . . . . "brand name"@en . . . . . . . "An entity, either biologic or otherwise, of interest in an investigation. [def-source: NCI]"@en . "Damion Dooley"@en . "NCIT Thesaurus"@en . "investigative subject"@en . . . "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" . "http://semanticscience.org/resource/SIO_000665"@en . . . . "antimicrobial resistance testing method"@en . . . . . "E-test (Epsilometry)"@en . . . . . "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" . . . . . . . . . . "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" . . . . . . . "http://purl.obolibrary.org/obo/ncit.owl"^^ . . . "organization name"@en . . "Damion Dooley"@en . "NCI Thesaurus"@en . . . . . "antibiotic treatment"@en . . . "fetal death (miscarriage/still birth)"@en . . _:genid527 . _:genid527 . _:genid527 . _:genid527 . . . . "NCBI SRA: 454 GS 20" . . "NCBI SRA: AB SOLiD System" . . "NCBI SRA: 454 GS FLX" . . "NCBI SRA: Illumina Genome Analyzer II" . . "NCBI SRA: Helicos HeliScope" . . . "pathogen role" . _:genid528 . _:genid529 . _:genid531 _:genid530 . _:genid529 _:genid531 . _:genid530 . _:genid530 . _:genid530 . _:genid531 . _:genid528 _:genid529 . _:genid528 . "Note: testing use of 'transmitted by' relation; issue to be resolved is whether appropriate domain and range are involved. This use would place 'transmitted by' as a subclass of 'participates in'"@en . _:genid532 . _:genid532 . _:genid532 . _:genid532 . . _:genid533 . _:genid533 . _:genid533 . _:genid533 . _:genid534 . _:genid535 . _:genid537 _:genid536 . _:genid535 _:genid537 . _:genid536 . _:genid536 . _:genid538 . _:genid539 . _:genid540 . _:genid539 _:genid540 . _:genid540 . _:genid538 _:genid539 . _:genid536 _:genid538 . _:genid537 . _:genid534 _:genid535 . _:genid534 . "Damion Dooley note: OBI has a variety of subclasses like \"blood specimen\" and \"colon specimen\" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic \"derives from some [uberon term]\". GenEpiO takes a different approach in describing this class with lists for \"subject anatomical site\", \"subject body product\", and \"plant anatomy\"."@en . . "^SAM[NED](\\w)?\\d+$"^^ . "http://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000350"^^ . "http://www.ncbi.nlm.nih.gov/Sequin/acc.html"^^ . "https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/"^^ . . _:genid541 . _:genid541 . _:genid541 . _:genid541 . _:genid542 . _:genid542 . _:genid542 . _:genid542 . _:genid543 . _:genid543 . _:genid543 . _:genid543 . "NCBI BioProject" . _:genid544 . _:genid544 . _:genid544 . _:genid545 . _:genid545 . _:genid545 . _:genid544 _:genid545 . _:genid544 "Project Description"@en . _:genid546 . _:genid546 . _:genid546 . _:genid547 . _:genid547 . _:genid547 . _:genid546 _:genid547 . _:genid546 "Description*" . "sample identifier"@en . . "specimen collection date"@en . . "help:Latitude should not be abstracted to the centre of a city, province/state or country as this may falsely implicate an existing location."@en . "Damion Dooley's note: IAO lat/long can't be made a subclass of \"angular coordinate\" or disjoint contradiction arises."@en . "See http://www.csgnetwork.com/gpscoordconv.html\n\nSee http://www.geomidpoint.com/latlon.html\nSee http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0001621\nSee http://www.w3.org/2003/01/geo/wgs84_pos"@en . . . _:genid548 . _:genid548 . _:genid548 . _:genid548 . "NCBI BioProject" . "NIAID GSCID-BRC" . . _:genid549 . _:genid549 . _:genid549 . _:genid549 . "Damion Dooley's note: A 'sovereign state' entity should have attribute or relationships to measurables - population, size, name, etc. So e.g. \" 'country name' inheres in some 'sovereign state/country'\".\n\nAlso note historical name issue (Myanmar vs Burma) and diplomatic name issue (Taiwan vs \"Republic of China\"). Both point to needing a single entity with multiple names."@en . "http://purl.obolibrary.org/obo/OMIABIS_0000006"^^ . "target material"@en . "NCBI BioProject: Material" . "Used in NCBI BioProject specifcation"@en . "specimen sample scope"@en . . . . . "sequencing facility"@en . . "project objective"@en . "NCBI BioProject: Objective" . . . "project method"@en . . "specimen provider PI email"@en . . _:genid550 . _:genid550 . _:genid550 . _:genid550 . _:genid551 . _:genid551 . _:genid551 "1"^^ . _:genid551 . _:genid551 . "categorical"@en . "scalar"@en . "Damion Dooley's note: \nOften a value specification may need to allow for a \"data item state\" that indicates that a given datum doesn't have a recorded or observed or retrievable value, and the general reason for this state."@en . . . "Assembly QC"@en . "Damion Dooley"@en . "http://www.nature.com/nature/journal.../409860a0.html"^^ . "GENEPIO"@en . . . . "NCBI SRA: Illumina MiSeq" . . "NCBI SRA: PacBio RS" . . "NCBI SRA: Illumina NextSeq" . . . . . . _:genid552 . _:genid552 . _:genid552 . _:genid552 . "sample"@en . . . . . "2019-09-08T23:41:09Z"^^ . "diagnosis"@en . . . "An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism."@en . "extended organism"@en . . . . "Damion Dooley" . . "NIAID: Comorbidity" . "complications"@en . _:genid553 . _:genid553 . _:genid553 . _:genid553 . _:genid553 "Comorbidity" . . . . . . . . . . . "http://purl.obolibrary.org/obo/omit"^^ . . . . . . . . . "Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable."@en . "Damion Dooley"@en . "grave"@en . . . . . . . "A type of Shiga toxin found in E. coli"@en . "Damion Dooley"@en . "Stx1"^^ . . . . "Shiga toxin 1"@en . . . . "A type of Shiga toxin found in E. coli which is antigenically distinct from Shiga toxin 1"@en . "Damion Dooley"@en . "Stx2"^^ . . . . "Shiga toxin 2"@en . . . . . "MLST typing"@en . . . . . _:genid554 . _:genid554 . _:genid554 . _:genid554 . . . . "A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments."@en . "physician role"@en . . . "Damion's Note: Future use might prefer: CMO_0000015 body temperature."@en . . "NCBI BioSample: female"@en . . "NCBI BioSample: male" . . . "Phenotypic sex refers to an individual's sex as determined by their internal and external genitalia, expression of secondary sex characteristics, and behavior."@en . "Note that NCBI Biosample has these values allowed:\nmale | female | pooled male and female | neuter | hermaphrodite | intersex | not determined | missing | not applicable | not collected"@en . "NCBI: http://www.ncbi.nlm.nih.gov/books/NBK10943/" . . "Damion Dooley's note: We can't say radius is a subclass of \"linear coordinate\" because length is considered a quality/specifically dependent continuant, which is disjoint with immaterial entity/independent continuant . I.e. \"length\" as quality unfortunately can't pertain to abstract entities, only \"real\" ones."@en . . . . . "social gathering"@en . . . . . . _:genid555 . _:genid555 . _:genid555 . _:genid555 . _:genid556 . _:genid556 . _:genid556 . _:genid556 . . "Damion Dooley" . . . _:genid557 . _:genid557 . _:genid557 . _:genid557 . _:genid558 . _:genid558 . _:genid558 "1"^^ . _:genid558 . _:genid558 . "sequence assembly"@en . "http://edamontology.org/data_0925"^^ . "http://purl.obolibrary.org/obo/OBI_0000973 - 'sequence data'"@en . . . . "Damion Dooley" . . . . . _:genid559 . _:genid559 . _:genid559 . _:genid559 . . "http://purl.obolibrary.org/obo/ERO_0002173"^^ . . . . . . . . . . . . "Damion Dooley's note: Unfortunately an IAO \"count\" cannot be a subclass of immaterial entity \"linear coordinate\" as this leads to disjoint conflict."@en . "Damion Dooley's note: A count datum often implicity carries a date range for which the count is ascertained, or estimated, or simulated for."@en . "Damion Dooley's note: The result of the act of counting is a scalar number whose unit is a description of the thing being counted. One can count 10 oranges and compare that to a count of 5 oranges. One can generalize that a count of 5 oranges is a count of pieces of fruit. One can then compare 5 oranges and 5 apples, fruitfully!"@en . . . . . . . . . . . . . . . . . . . . . . . "variable type"@en . . . . . . _:genid560 . _:genid561 . _:genid563 _:genid562 . _:genid561 _:genid563 . _:genid562 . _:genid562 . _:genid562 . _:genid565 _:genid564 . _:genid563 _:genid565 . _:genid564 . _:genid564 . _:genid564 . _:genid567 _:genid566 . _:genid565 _:genid567 . _:genid566 . _:genid566 . _:genid566 . _:genid567 . _:genid560 _:genid561 . _:genid560 . . "A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host."@en . "https://www.ebi.ac.uk/ols/ontologies/trans"^^ . "TRANS follows the CDC Epidemiology model of transmission between two hosts, a reservoir and host or other non-host, non-reservoir entities (e.g), a needle and a host."@en . "transmission of infection"@en . . . "Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission."@en . "https://www.ebi.ac.uk/ols/ontologies/trans"^^ . "direct transmission"@en . . . "Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles."@en . "https://www.ebi.ac.uk/ols/ontologies/trans"^^ . "indirect transmission"@en . . . "Congenital transmission is a direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth."@en . "https://www.ebi.ac.uk/ols/ontologies/trans"^^ . "congenital"@en . . . "contact transmission"@en . "Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen."@en . "https://www.ebi.ac.uk/ols/ontologies/trans"^^ . "contact"@en . . . "Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking."@en . "https://www.ebi.ac.uk/ols/ontologies/trans"^^ . "droplet spread"@en . . . "Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products."@en . "https://www.ebi.ac.uk/ols/ontologies/trans"^^ . "vehicle-born ingestion"@en . . . . . . . _:genid568 . _:genid568 . _:genid568 . _:genid568 . "organism body product"@en . . . . . . . . . . . . . . . . . . . . . . "poultry fluff"@en . "Damion Dooley's note: Poultry fluff is both an 'anatomical structure' and a body product when it is shed."@en . . . . "Damion Dooley's note: Need to build this out further with reference to http://unitsofmeasure.org/trac and other unit ontologies: \n \n[1] R. Hodgson and P. J. Keller, \"QUDT-quantities, units, dimensions and data types in OWL and XML.\" Online (September 2011) http://www. qudt.org\n[2] M. van Assem, H. Rijgersberg, and J. Top, \"Ontology of units of measure and related concepts.\" Semantic Web 4, no. 1 (2013): 3-13.\n[3] G. V. Gkoutos, P. N. Schofield, and R. Hoehndorf, \"The Units Ontology: a tool for integrating units of measurement in science.\" Database2012 (2012): bas033."@en . . "mm"^^ . . . . . "\u00B5g/ml"^^ . . . . . . . "ongoing pregnancy"@en . . . "ancestral group"@en . . . "Damion Dooley" . . . _:genid569 . _:genid569 . _:genid569 . _:genid569 . _:genid570 . _:genid570 . _:genid570 . _:genid570 . "requires discussion"@en . "A personal health datum which specifies host role at time of specimen collection."@en . "0000-0002-9578-0788" . "2022-01-31T23:53:59Z"^^ . "host role at time of specimen collection" . . . . "MLVA typing"@en . . . _:genid571 . _:genid571 . _:genid571 . _:genid571 . "Damion Dooley's comment: On spheroids a polygon can be minimally defined by latitude and longitude coordinates, however technically this is ambiguous whether the larger or smaller area is being referred to. Unambiguously, such a polygon could be defined by an epicenter, and a latitude width and longitude height."@en . . . "In elementary geometry, a polygon is a plane figure that is bounded by a finite chain of straight line segments closing in a loop to form a closed chain or circuit."@en . "Damion Dooley" . "https://en.wikipedia.org/wiki/Polygon" . . . . . . . "PulseNet: Key"@en . . . . . . . . "Damion Dooley" . "medical health record (history / timeline)"@en . . . _:genid572 . _:genid573 . _:genid574 . _:genid573 _:genid574 . _:genid574 . _:genid572 _:genid573 . _:genid572 . . "depth:1" . "lookup" . . . . "Bacterial bacteriophage typing"@en . "http://phinvads.cdc.gov/vads/http:/phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.6.96&code=22642004" . . . . "http://purl.obolibrary.org/obo/hancestro_0004"^^ . "obsolete: ancestral group"@en . "true"^^ . . . . . . . . _:genid575 . _:genid575 . _:genid575 . _:genid575 . "A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP)"@en . . . . . "Welcome to the GenEpiO ontology! The \"information content entity\" class has many GenEpiO terms. \"data item > measurement data item\" has many datum terms; see \"data representational model\" for collections of terms set up for compatibility with 3rd party sources.\n\nNote that this file contains examples of cities, provinces, states, territories, and soverign nations from around the world; customization of this geographical content would be expected for particular regional use."@en . . . . . . . . "Base class for definitions."@en . . . "A named element in the model."@en . . . "Usage example and description."@en . . . "An attributed label."@en . . . "A permissible value, accompanied by intended text and an optional mapping to a concept URI."@en . . . "A collection of subset, type, slot and class definitions."@en . . . "The definition of a property or a slot."@en . . . . . . . . . . . . "Damion Dooley" . "Damion Dooley's note: Here we are exploring the use of individuals/instances to describe local picklists for GenEpiO driven software."@en . . . . . . . . . . . . "United Nations"@en . . "MSH"@en . . "NCI_Thesaurus"@en . . "NIFSTD"@en . . "home"@en . . "_test_individual"@en . . . "LabID assigned by NLEP"@en . "Damion Dooley"^^ . "2019-04-17T23:31:44Z"^^ . "PulseNet:LabID"@en . . "Country where isolate was collected"@en . "Damion Dooley"^^ . "2019-04-17T23:32:45Z"^^ . "SourceCountry"@en . . . "Country where isolate was collected"@en . "Currently not used for PulseNet Canada"@en . "Damion Dooley"^^ . "2019-04-17T23:37:19Z"^^ . "PulseNet:SourceCountry"@en . . . "(Province for PNC) where isolate was collected."@en . "Damion Dooley"^^ . "2019-04-17T23:38:09Z"^^ . "PulseNet:SourceState"@en . . . "Damion Dooley"^^ . "2019-04-17T23:40:57Z"^^ . "PulseNet:SourceCity"@en . . . "Site of the source type where isolate was collected, e.g. blood, CSF, etc."@en . "Damion Dooley"^^ . "2019-04-17T23:47:10Z"^^ . "PulseNet:SourceSite"@en . . . "The source type of the isolate, e.g. human, environmental, etc."@en . "Damion Dooley"^^ . "2019-04-17T23:48:49Z"^^ . "PulseNet:SourceType"@en . . . "Other countries where the patient traveled"@en . "Damion Dooley"^^ . "2019-04-17T23:49:47Z"^^ . "PulseNet:Traveled_To"@en . . . "Further description of the source type, e.g. bovine, chicken"@en . "Damion Dooley"^^ . "2019-04-17T23:51:02Z"^^ . "PulseNet:TypeDetails"@en . . . "Submitted isolate # (if diff. From Key #), NLEP will enter Prov. Submitted # if sample was sent to NLEP for PFGE"@en . "Damion Dooley"^^ . "2019-04-17T23:52:01Z"^^ . "PulseNet:SubmittedNumber"@en . . . "(Province for PNC) additional number used to identify the isolate"@en . "Damion Dooley"^^ . "2019-04-17T23:53:47Z"^^ . "PulseNet:OtherStateIsolate"@en . . . "Age of patient when isolate was collected"@en . "Damion Dooley"^^ . "2019-04-17T23:54:24Z"^^ . "PulseNet:PatientAge"@en . . . "Sex of patient when isolate was collected"@en . "Damion Dooley"^^ . "2019-04-17T23:55:04Z"^^ . "PulseNet:PatientSex"@en . . . . "Date of collection"@en . "Damion Dooley"^^ . "2019-04-17T23:56:33Z"^^ . "PulseNet:IsolatDate"@en . . . "Date the isolate is uploaded to the national database after initial upload"@en . "Damion Dooley"^^ . "2019-04-18T00:21:46Z"^^ . "PulseNet:UploadModifiedDate"@en . . . "Antigenic Formula"@en . "Damion Dooley"^^ . "2019-04-18T00:23:18Z"^^ . "PulseNet:AntigenForm"@en . . . "Subspecies, I - VI (roman numerals)"@en . "Damion Dooley"^^ . "2019-04-18T00:24:11Z"^^ . "PulseNet:Subspecies"@en . . . "O polysaccharide (LPS) Group"@en . "Damion Dooley"^^ . "2019-04-18T00:24:53Z"^^ . "PulseNet:OGroup"@en . . . "Serotype of isolate"@en . "Damion Dooley"^^ . "2019-04-18T00:25:22Z"^^ . "PulseNet:Serotype"@en . . . "Code issued by CDC; see: 'Naming of outbreaks\u2026' on WebBoard. (format YYMMLabIDLITScode-#)"@en . "Currently not used for PulseNet Canada"@en . "Damion Dooley"^^ . "2019-04-18T00:27:08Z"^^ . "PulseNet:Outbreak"@en . . . "Number issued by CDC if isolate is run at CDC (Key will be # issued by NLEP if isolate run at NLEP)"@en . "Damion Dooley"^^ . "2019-04-18T00:28:01Z"^^ . "PulseNet:cdc_id"@en . . . "Enzyme name present if part of that national list."@en . "Damion Dooley"^^ . "2019-04-18T00:28:35Z"^^ . "PulseNet:ListMember"@en . . . "Phage type"@en . "Damion Dooley"^^ . "2019-04-18T00:29:20Z"^^ . "PulseNet:Phagetype"@en . . . "Provides LabID, gel and lane information"@en . "Damion Dooley"^^ . "2019-04-18T00:29:58Z"^^ . "PulseNet:TEMP"@en . . . "Status of the isolate; this is only confirmed once CDC runs it."@en . "Currently not used for PulseNet Canada"@en . "Damion Dooley"^^ . "2019-04-18T00:30:44Z"^^ . "PulseNet:Status"@en . . . "Currently not used for PulseNet Canada"@en . "checked if the isolate is part of NARMS."@en . "Damion Dooley"^^ . "2019-04-18T00:35:55Z"^^ . "PulseNet:NARMS-EB"@en . . . "Checked if the isolate is part of FoodNet."@en . "Currently not used for PulseNet Canada"@en . "Damion Dooley"^^ . "2019-04-18T00:36:39Z"^^ . "PulseNet:FoodNet"@en . . . "XbaI gel where the isolate is located, lane of gel"@en . "Damion Dooley"^^ . "2019-04-18T00:38:57Z"^^ . "PulseNet:PFGE-XbaI-file"@en . . . "XbaI pattern assigned by CDC (format XXXXXX.####)"@en . "Damion Dooley"^^ . "2019-04-18T00:39:23Z"^^ . "PulseNet:PFGE-XbaI-pattern"@en . . . "The date the XbaI gel is run"@en . "Damion Dooley"^^ . "2019-04-18T00:40:05Z"^^ . "PulseNet:PFGE-XbaI-rundate"@en . . . "Once the XbaI pattern is named, the status is confirmed by CDC"@en . "Damion Dooley"^^ . "2019-04-18T00:41:39Z"^^ . "PulseNet:PFGE-XbaI-status"@en . . . "BlnI gel where the isolate is located, lane of gel"@en . "Damion Dooley"^^ . "2019-04-18T00:42:11Z"^^ . "PulseNet:PFGE-BlnI-file"@en . . . "BlnI pattern assigned by CDC (format XXXXXX.####)."@en . "Damion Dooley"^^ . "2019-04-18T00:42:42Z"^^ . "PulseNet:PFGE-BlnI-pattern"@en . . . "The date the BlnI gel is run"@en . "Damion Dooley"^^ . "2019-04-18T00:43:50Z"^^ . "PulseNet:PFGE-BlnI-rundate"@en . . . "Once the BlnI pattern is named, the status is confirmed by CDC"@en . "Damion Dooley"^^ . "2019-04-18T00:44:44Z"^^ . "PulseNet:PFGE-BlnI-status"@en . . . "SpeI gel where the isolate is located, lane of gel."@en . "Damion Dooley"^^ . "2019-04-18T00:45:15Z"^^ . "PulseNet:PFGE-SpeI-file"@en . . . "SpeI pattern assigned by CDC (format XXXXXX.####)."@en . "Damion Dooley"^^ . "2019-04-18T00:45:41Z"^^ . "PulseNet:PFGE-SpeI-pattern"@en . . . "The date the SpeI gel is run."@en . "Damion Dooley"^^ . "2019-04-18T00:46:21Z"^^ . "PulseNet:PFGE-SpeI-rundate"@en . . . "Once the SpeI pattern is named, the status is confirmed by CDC."@en . "Damion Dooley"^^ . "2019-04-18T00:47:00Z"^^ . "PulseNet:PFGE-SpeI-status"@en . . . "Date WHICH (PH?) lab received isolate."@en . "Damion Dooley"^^ . "2019-04-18T00:57:28Z"^^ . "PulseNet:ReceivedDate"@en . . . . "2019-11-17T00:54:44Z"^^ . "ISO_23418.organization_contact.service"@en . . . "Date the isolate uploaded to the national database."@en . "Damion Dooley"^^ . "2019-04-17T22:47:51Z"^^ . "PulseNet:UploadDate"@en . _:genid576 "2"^^ . _:genid577 "2"^^ . "I"@en . "intermediate"@en . "R"@en . "resistant"@en . "S"@en . "sensitive"@en . "susceptible"@en . "NS"@en . "nonsensitive"@en . "nonsusceptible"@en . "sensitive - dose dependent"@en . "susceptible - dose dependent"@en . "SSD"@en . "BSAC"^^ . "DIN"^^ . "EUCAST"^^ . "SFM"^^ . "Damion Dooley's note: this BFO class is incompatible with \"immaterial entity\" \"n-dimensional concept\"."@en . "food role"@en . "constructed feature"@en . "http://purl.obolibrary.org/obo/NCIT_C25464"@en . "irrigation pond"@en . "http://purl.obolibrary.org/obo/NCIT_C80234"@en . "stool"@en . "http://opendata.inra.fr/EOL/EOL_0001601#bedding"^^ . "straw bedding"@en . "true"^^ . "chicken cage"@en . "NCBI SRA: ION_TORRENT" . "asian tiger shrimp"@en . "black tiger shrimp"@en . "wild"@en . "gathered"@en . "Damion Dooley" . . "This is a catch-all category for Gazetteer items that have \"located in\" relations but not an imported GAZETTEER class parent in GenEpiO."@en . "Damion Dooley" . "true"^^ . . "Damion Dooley"@en . "obsolete: has primitive data type"@en . . "Damion Dooley" . . "Damion Dooley" . . "Damion Dooley" . "Damion Dooley" . . "Damion Dooley" . . . "Damion Dooley" . . "Damion Dooley" . "Damion Dooley's note: IAO lat/long can't be made a subclass of \"angular coordinate\" or disjoint contradiction arises with \"immaterial entity\""@en . "Damion Dooley" . . . "Damion Dooley" . . "Damion Dooley" . "Damion Dooley" . . . "Damion Dooley" . "Damion Dooley" . . "Damion Dooley" . "This seems to be covered by 'datetime range intermediate'"@en . . "Damion Dooley" . . "Damion Dooley" . . "Damion Dooley" . "A datetime set item is a datetime that has been grouped semantically under a given type of process"@en . "Damion Dooley" . . "Damion Dooley" . . "Damion Dooley" . . "Damion Dooley" . . "Damion Dooley" . . "Damion Dooley" . . "mobile"@en . "work"@en . . "Damion Dooley" . . "An unordered set is a set of elements which have no intrinsic (semantic) order with respect to each other. The set of all living people is not intrinsically ordered; an ordering can only be provided by looking at some partiular feature of the given set elements."@en . "Damion Dooley" . . "Damion Dooley" . "Damion Dooley" . . . "Damion Dooley" . "Damion Dooley" . . "https://en.wikipedia.org/wiki/Plane_(geometry)"^^ . "Damion Dooley" . . "clam, squid, octopus"@en . "NCBI SRA: HELICOS" . "NCBI SRA: ABI_SOLID" . "A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement."@en . "specimen provider PI organization"@en . "NCBI SRA: Illumina Genome Analyzer IIx" . "NCBI SRA: AB SOLiD 3 Plus System" . "NCBI SRA: AB SOLiD 4 System" . "NCBI SRA: Illumina Genome Analyzer IIe" . "disease (OGMS)"@en . . "NCBI BioSample: hermaphrodite" . "This value is not present in NCBI BioSample host sex."@en . "derives into"@en . "starts during"@en . "happens during"@en . "starts with"@en . "ends with"@en . "input of"@en . "Damion Dooley's note:Damion Dooley's note: Outstanding issue: How to attach units to each dimension? This depends on the instance of the problem involving a dimension?\n\nLinear offset can be decimal or integer or complex, or a count.\n - Can have a unit: meter, kilometer, foot, light-year, oranges, apples, fruit\n\nAngular offset can be radians or degrees."@en . "n-dimensional coordinate system"@en . "rectal"@en . "http://purl.obolibrary.org/obo/BTO_0000818"^^ . "cerebrospinal fluid (CSF)"@en . "Damion Dooley" . . "cfu/mL" . "Damion Dooley"@en . . "http://purl.obolibrary.org/obo/PATO_0000011"^^ . _:genid578 . _:genid579 . _:genid580 . _:genid579 _:genid580 . _:genid581 . _:genid580 _:genid581 . _:genid582 . _:genid581 _:genid582 . _:genid582 . _:genid578 _:genid579 . _:genid583 . _:genid584 . _:genid585 . _:genid584 _:genid585 . _:genid586 . _:genid585 _:genid586 . _:genid587 . _:genid586 _:genid587 . _:genid587 . _:genid583 _:genid584 . _:genid588 . _:genid589 . _:genid590 . _:genid589 _:genid590 . _:genid591 . _:genid590 _:genid591 . _:genid592 . _:genid591 _:genid592 . _:genid593 . _:genid592 _:genid593 . _:genid594 . _:genid593 _:genid594 . _:genid595 . _:genid594 _:genid595 . _:genid596 . _:genid595 _:genid596 . _:genid597 . _:genid596 _:genid597 . _:genid598 . _:genid597 _:genid598 . _:genid599 . _:genid598 _:genid599 . _:genid600 . _:genid599 _:genid600 . _:genid601 . _:genid600 _:genid601 . _:genid602 . _:genid601 _:genid602 . _:genid603 . _:genid602 _:genid603 . _:genid604 . _:genid603 _:genid604 . _:genid605 . _:genid604 _:genid605 . _:genid606 . _:genid605 _:genid606 . _:genid607 . _:genid606 _:genid607 . _:genid608 . _:genid607 _:genid608 . _:genid609 . _:genid608 _:genid609 . _:genid610 . _:genid609 _:genid610 . _:genid611 . _:genid610 _:genid611 . _:genid612 . _:genid611 _:genid612 . _:genid613 . _:genid612 _:genid613 . _:genid614 . _:genid613 _:genid614 . _:genid615 . _:genid614 _:genid615 . _:genid616 . _:genid615 _:genid616 . _:genid617 . _:genid616 _:genid617 . _:genid618 . _:genid617 _:genid618 . _:genid619 . _:genid618 _:genid619 . _:genid620 . _:genid619 _:genid620 . _:genid621 . _:genid620 _:genid621 . _:genid622 . _:genid621 _:genid622 . _:genid623 . _:genid622 _:genid623 . _:genid624 . _:genid623 _:genid624 . _:genid625 . _:genid624 _:genid625 . _:genid626 . _:genid625 _:genid626 . _:genid627 . _:genid626 _:genid627 . _:genid628 . _:genid627 _:genid628 . _:genid628 . _:genid588 _:genid589 .