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‎_config.yml‎

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@@ -2135,6 +2135,59 @@ ontologies:
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label: Fungal
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title: Fungal gross anatomy
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tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues
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- activity_status: active
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build:
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checkout: git clone https://github.com/foundingGIDE/fbbi.git
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path: .
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system: git
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contact:
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email: damien@gerbi-gmb.de
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github: gouttegd
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label: Damien Goutte-Gattat
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orcid: 0000-0002-6095-8718
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dependencies:
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- id: iao
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- id: omo
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- id: ro
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description: An ontology for the description of sample preparation, visualization,
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and imaging methods used in biomedical research.
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domain: investigations
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homepage: https://github.com/foundingGIDE/fbbi
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id: fbbi
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layout: ontology_detail
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license:
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label: CC BY 4.0
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logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
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url: https://creativecommons.org/licenses/by/4.0/
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ontology_purl: http://purl.obolibrary.org/obo/fbbi.owl
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preferredPrefix: FBbi
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products:
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- id: fbbi.owl
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ontology_purl: http://purl.obolibrary.org/obo/fbbi.owl
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- id: fbbi.obo
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ontology_purl: http://purl.obolibrary.org/obo/fbbi.obo
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- id: fbbi/fbbi-base.owl
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ontology_purl: http://purl.obolibrary.org/obo/fbbi/fbbi-base.owl
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- id: fbbi/fbbi-base.obo
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ontology_purl: http://purl.obolibrary.org/obo/fbbi/fbbi-base.obo
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repository: https://github.com/foundingGIDE/fbbi
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tags:
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- imaging experiments
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title: Biological Imaging Methods Ontology
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tracker: https://github.com/foundingGIDE/fbbi/issues
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usages:
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- description: FlyBase uses FBbi to annotate its image collection.
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examples:
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- description: images annotated to "scanning electron micrograph"
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url: https://flybase.org/cgi-bin/fbcvquery.pl?mode=subtreehits&cvterm=FBbi:00000257%3EFBim
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user: https://flybase.org
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- description: Virtual Fly Brain uses FBbi to annotate images.
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user: https://virtualflybrain.org
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- description: The Cell Image Library uses FBbi to annotate images.
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examples:
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- description: An image annotate with several terms from FBbi.
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url: https://www.cellimagelibrary.org/images/13654
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user: https://www.cellimagelibrary.org
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- activity_status: active
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browsers:
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- label: FB
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platform for integrating, mining and analyzing microbiome experiments.
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type: annotation and query
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user: https://microbiomedb.org
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- activity_status: inactive
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build:
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method: obo2owl
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source_url: https://raw.githubusercontent.com/dosumis/fbbi/master/src/ontology/fbbi.obo
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contact:
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email: wawong@gmail.com
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github: wawong
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label: Willy Wong
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orcid: 0000-0002-8841-5870
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description: A structured controlled vocabulary of sample preparation, visualization
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and imaging methods used in biomedical research.
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domain: investigations
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homepage: http://cellimagelibrary.org/
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id: fbbi
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layout: ontology_detail
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license:
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label: CC BY 4.0
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logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
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url: https://creativecommons.org/licenses/by/4.0/
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ontology_purl: http://purl.obolibrary.org/obo/fbbi.owl
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preferredPrefix: FBbi
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products:
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- id: fbbi.owl
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ontology_purl: http://purl.obolibrary.org/obo/fbbi.owl
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repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology
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tags:
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- imaging experiments
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title: Biological Imaging Methods Ontology
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tracker: https://github.com/CRBS/Biological_Imaging_Methods_Ontology/issues
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- activity_status: inactive
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contact:
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email: druzinsk@uic.edu

‎principles/fp-000-summary.md‎

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@@ -24,9 +24,9 @@ P5) <b>Scope</b> - The scope of an ontology is the extent of the domain or subje
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P6) <b>Textual Definitions</b> - The ontology MUST have textual definitions for the majority of its classes and for top level terms in particular.
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P7) <b>Relations</b> - Relations SHOULD be reused from the Relations Ontology (RO).
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P7) <b>Relations</b> - Existing relations MUST be reused. New relations SHOULD be submitted to the Relations Ontology (RO).
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P8) <b>Documentation</b> - The owners of the ontology SHOULD strive to provide as much documentation as possible.
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P8) <b>Documentation</b> - The owners of the ontology SHOULD strive to provide as much documentation as possible. The documentation SHOULD detail the different processes specific to an ontology life cycle and target various audiences (users or developers).
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P9) <b>Documented Plurality of Users</b> - The ontology developers SHOULD document that the ontology is used by multiple independent people or organizations.
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‎principles/fp-008-documented.md‎

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@@ -10,7 +10,7 @@ The wording of this principle is still in progress, with some issues still to be
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## Summary
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The owners of the ontology should strive to provide as much documentation as possible. The documentation should detail the different processes specific to an ontology life cycle and target various audiences (users or developers).
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The owners of the ontology SHOULD strive to provide as much documentation as possible. The documentation SHOULD detail the different processes specific to an ontology life cycle and target various audiences (users or developers).
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[This check is automatically validated.](checks/fp_008)
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‎principles/fp-009-users.md‎

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@@ -7,8 +7,7 @@ GO TO: [Recommendations/Requirements](#recommendations-and-requirements) &#124;
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## Summary
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The ontology developers should document that the ontology is used by
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multiple independent people or organizations.
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The ontology developers SHOULD document that the ontology is used by multiple independent people or organizations.
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## Purpose
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‎registry/obo_prefixes.ttl‎

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,[ sh:prefix "EXMO" ; sh:namespace "http://purl.obolibrary.org/obo/EXMO_"]
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,[ sh:prefix "ExO" ; sh:namespace "http://purl.obolibrary.org/obo/ExO_"]
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,[ sh:prefix "FAO" ; sh:namespace "http://purl.obolibrary.org/obo/FAO_"]
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,[ sh:prefix "FBbi" ; sh:namespace "http://purl.obolibrary.org/obo/FBbi_"]
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,[ sh:prefix "FBbt" ; sh:namespace "http://purl.obolibrary.org/obo/FBbt_"]
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,[ sh:prefix "FBcv" ; sh:namespace "http://purl.obolibrary.org/obo/FBcv_"]
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,[ sh:prefix "FBdv" ; sh:namespace "http://purl.obolibrary.org/obo/FBdv_"]
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,[ sh:prefix "SIBO" ; sh:namespace "http://purl.obolibrary.org/obo/SIBO_"]
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,[ sh:prefix "VariO" ; sh:namespace "http://purl.obolibrary.org/obo/VariO_"]
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,[ sh:prefix "EUPATH" ; sh:namespace "http://purl.obolibrary.org/obo/EUPATH_"]
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,[ sh:prefix "FBbi" ; sh:namespace "http://purl.obolibrary.org/obo/FBbi_"]
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,[ sh:prefix "MFMO" ; sh:namespace "http://purl.obolibrary.org/obo/MFMO_"]
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,[ sh:prefix "MICRO" ; sh:namespace "http://purl.obolibrary.org/obo/MICRO_"]
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,[ sh:prefix "OGSF" ; sh:namespace "http://purl.obolibrary.org/obo/OGSF_"]

‎registry/ontologies.jsonld‎

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"title": "Fungal gross anatomy",
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"tracker": "https://github.com/obophenotype/fungal-anatomy-ontology/issues"
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},
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{
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"activity_status": "active",
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"build": {
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"checkout": "git clone https://github.com/foundingGIDE/fbbi.git",
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"path": ".",
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"system": "git"
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},
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"contact": {
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"email": "damien@gerbi-gmb.de",
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"github": "gouttegd",
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"label": "Damien Goutte-Gattat",
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"orcid": "0000-0002-6095-8718"
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},
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"dependencies": [
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{
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"id": "iao"
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},
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{
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"id": "omo"
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},
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{
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"id": "ro"
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}
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],
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"description": "An ontology for the description of sample preparation, visualization, and imaging methods used in biomedical research.",
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"domain": "investigations",
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"homepage": "https://github.com/foundingGIDE/fbbi",
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"id": "fbbi",
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"layout": "ontology_detail",
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"license": {
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"label": "CC BY 4.0",
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"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
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"url": "https://creativecommons.org/licenses/by/4.0/"
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},
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"ontology_purl": "http://purl.obolibrary.org/obo/fbbi.owl",
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"preferredPrefix": "FBbi",
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"products": [
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{
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"id": "fbbi.owl",
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"ontology_purl": "http://purl.obolibrary.org/obo/fbbi.owl"
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},
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{
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"id": "fbbi.obo",
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"ontology_purl": "http://purl.obolibrary.org/obo/fbbi.obo"
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},
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{
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"id": "fbbi/fbbi-base.owl",
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"ontology_purl": "http://purl.obolibrary.org/obo/fbbi/fbbi-base.owl"
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},
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{
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"id": "fbbi/fbbi-base.obo",
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"ontology_purl": "http://purl.obolibrary.org/obo/fbbi/fbbi-base.obo"
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}
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],
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"repository": "https://github.com/foundingGIDE/fbbi",
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"tags": [
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"imaging experiments"
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],
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"title": "Biological Imaging Methods Ontology",
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"tracker": "https://github.com/foundingGIDE/fbbi/issues",
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"usages": [
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{
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"description": "FlyBase uses FBbi to annotate its image collection.",
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"examples": [
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{
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"description": "images annotated to \"scanning electron micrograph\"",
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"url": "https://flybase.org/cgi-bin/fbcvquery.pl?mode=subtreehits&cvterm=FBbi:00000257%3EFBim"
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}
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],
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"user": "https://flybase.org"
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},
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{
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"description": "Virtual Fly Brain uses FBbi to annotate images.",
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"user": "https://virtualflybrain.org"
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},
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{
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"description": "The Cell Image Library uses FBbi to annotate images.",
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"examples": [
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{
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"description": "An image annotate with several terms from FBbi.",
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"url": "https://www.cellimagelibrary.org/images/13654"
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}
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],
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"user": "https://www.cellimagelibrary.org"
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}
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]
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},
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{
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"activity_status": "active",
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"browsers": [
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}
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]
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},
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{
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"activity_status": "inactive",
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"build": {
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"method": "obo2owl",
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"source_url": "https://raw.githubusercontent.com/dosumis/fbbi/master/src/ontology/fbbi.obo"
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},
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"contact": {
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"email": "wawong@gmail.com",
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"github": "wawong",
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"label": "Willy Wong",
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"orcid": "0000-0002-8841-5870"
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},
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"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
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"domain": "investigations",
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"homepage": "http://cellimagelibrary.org/",
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"id": "fbbi",
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"layout": "ontology_detail",
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"license": {
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"label": "CC BY 4.0",
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"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
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"url": "https://creativecommons.org/licenses/by/4.0/"
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},
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"ontology_purl": "http://purl.obolibrary.org/obo/fbbi.owl",
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"preferredPrefix": "FBbi",
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"products": [
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{
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"id": "fbbi.owl",
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"ontology_purl": "http://purl.obolibrary.org/obo/fbbi.owl"
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}
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],
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"repository": "https://github.com/CRBS/Biological_Imaging_Methods_Ontology",
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"tags": [
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"imaging experiments"
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],
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"title": "Biological Imaging Methods Ontology",
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"tracker": "https://github.com/CRBS/Biological_Imaging_Methods_Ontology/issues"
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},
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{
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"activity_status": "inactive",
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"contact": {

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