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Merge branch 'master' into nataled-patch-5
2 parents 5fe3f96 + db6d3ee commit 096430e

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Lines changed: 1685 additions & 1565 deletions

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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
@@ -8424,35 +8477,6 @@ ontologies:
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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

‎registry/obo_prefixes.ttl‎

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@@ -52,6 +52,7 @@
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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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