diff --git a/.gitmodules b/.gitmodules index dda7175..e69de29 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +0,0 @@ -[submodule "swagger-ui"] - path = swagger-ui - url = https://github.com/swagger-api/swagger-ui.git diff --git a/000-default.conf b/000-default.conf deleted file mode 100644 index eef2ea9..0000000 --- a/000-default.conf +++ /dev/null @@ -1,36 +0,0 @@ - - # The ServerName directive sets the request scheme, hostname and port that - # the server uses to identify itself. This is used when creating - # redirection URLs. In the context of virtual hosts, the ServerName - # specifies what hostname must appear in the request's Host: header to - # match this virtual host. For the default virtual host (this file) this - # value is not decisive as it is used as a last resort host regardless. - # However, you must set it for any further virtual host explicitly. - ServerName mijnvoorbeeld.com - - ServerAdmin webmaster@localhost - DocumentRoot /var/www/html - - ProxyPassMatch /swagger/ ! - ProxyPass "/" "http://172.17.0.2:8183/" - ProxyPassReverse "/" "http://172.17.0.2:8183/" - - # Available loglevels: trace8, ..., trace1, debug, info, notice, warn, - # error, crit, alert, emerg. - # It is also possible to configure the loglevel for particular - # modules, e.g. - #LogLevel info ssl:warn - - ErrorLog ${APACHE_LOG_DIR}/error.log - CustomLog ${APACHE_LOG_DIR}/access.log combined - - # For most configuration files from conf-available/, which are - # enabled or disabled at a global level, it is possible to - # include a line for only one particular virtual host. For example the - # following line enables the CGI configuration for this host only - # after it has been globally disabled with "a2disconf". - #Include conf-available/serve-cgi-bin.conf - - -# vim: syntax=apache ts=4 sw=4 sts=4 sr noet - diff --git a/Dockerfile b/Dockerfile index 037febc..181f8b5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,7 +5,6 @@ MAINTAINER BiGCaT ENV PORT 8080 RUN apt-get update -RUN apt-get install apache2 -y RUN apt-get install jq -y COPY setup.sh / @@ -19,28 +18,7 @@ RUN /setup.sh COPY startup.sh /opt/bridgedb/bridgedb/ RUN chmod +x /opt/bridgedb/bridgedb/startup.sh -COPY ports.conf /etc/apache2 -COPY 000-default.conf /etc/apache2/sites-enabled/ - -RUN a2enmod proxy \ -&& a2enmod proxy_http \ -&& a2enmod ssl \ -&& a2enmod rewrite \ -&& service apache2 stop - -COPY ports.conf /etc/apache2 -COPY 000-default.conf /etc/apache2/sites-enabled/ - -#improve with configuration change instead of copy -#CMD sed -i "s/80/$PORT/g" /etc/apache2/sites-available/000-default.conf -#CMD sed -i "s/80/$PORT/g" /etc/apache2/ports.conf - -RUN mkdir /var/www/html/swagger/ -COPY v3/ /var/www/html/swagger/ -COPY index.html /var/www/html/swagger/ -COPY bridgedb.png /var/www/html/swagger/ - EXPOSE 8183 8080 -ENTRYPOINT service apache2 start && /opt/bridgedb/bridgedb/startup.sh -f /opt/bridgedb-databases/gdb.config +ENTRYPOINT /opt/bridgedb/bridgedb/startup.sh -f /opt/bridgedb-databases/gdb.config CMD ["-D", "FOREGROUND"] diff --git a/index.html b/index.html deleted file mode 100644 index 47dab25..0000000 --- a/index.html +++ /dev/null @@ -1,63 +0,0 @@ - - - - - - Swagger UI - - - - - - - - -
- - - - - - diff --git a/setup.sh b/setup.sh index 049675b..9ee4633 100644 --- a/setup.sh +++ b/setup.sh @@ -9,7 +9,7 @@ #This line is updated at every run of https://github.com/bridgedb/docker/blob/master/.github/workflows/buildandpush.yml substituting the #bridgedbwsversion with the one declared in the bridgedbwservice pom (https://raw.githubusercontent.com/bridgedb/BridgeDbWebservice/main/pom.xml). #The changes are NOT committed and pushed, but are effective when running setup.sh in the action. -export BRIDGEDBWSVERSION="2.1.4" +export BRIDGEDBWSVERSION="2.1.6" cd /opt/ mkdir -p bridgedb/bridgedb/ diff --git a/startup.sh b/startup.sh index 6c1173f..e400a9e 100644 --- a/startup.sh +++ b/startup.sh @@ -9,8 +9,4 @@ cd $(dirname $0) # change to directory of this script pwd -apt install nmap -y -nmap localhost - -sed -i "s|SERVER_URL|$SERVER_URL|" /var/www/html/swagger/swagger.json -java -jar BridgeDb-Webservice.jar 8183 > bridgedb.log +java -jar BridgeDb-Webservice.jar 8183 true $SERVER_URL > bridgedb.log diff --git a/swagger-annotated.json b/swagger-annotated.json deleted file mode 100644 index 29f8e01..0000000 --- a/swagger-annotated.json +++ /dev/null @@ -1,1037 +0,0 @@ -{ - "swagger": "2.0", - "x-orn-@id": "https://bridgedb.prod.openrisknet.org", - "x-orn-@type": "x-orn:Service", - "info": { - "description": "BridgeDb is a framework to map identifiers between various biological databases. \nThese mappings are provided for genes, proteins, genetic variants, metabolites, and metabolic reactions.", - "version": "0.9.0", - "title": "BridgeDb identifier mapping service", - "name": "BridgeDb identifier mapping service", - "contact": { - "name": "Maastricht University", - "email": "marvin.martens@maastrichtuniversity.nl", - "url": "http://bridgedb.org" - } }, - - "consumes":["text/html"], - "produces":["*/*"], - "host": "", - "schemes": [ - "http" - ], - "paths": { - "/{organism}/xrefs/{systemCode}/{identifier}": { - "x-orn:path": "https://bridgedb.prod.openrisknet.org/{organism}/xrefs/{systemCode}/{identifier}", - "get": { - - "x-orn:path": "https://bridgedb.prod.openrisknet.org/{organism}/xrefs/{systemCode}/{identifier}", - "x-orn:method": "Get", - "description": "Returns a list of xrefs that map to a given identifier, data source, and organism.", - "x-orn:expects": { - "x-orn-@id": "x-orn:Descriptor", - "x-orn-@type": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks","Human", "Homo sapiens","Tuberculosis", "Mycobacterium tuberculosis","Mosquito", "Anopheles gambiae","Zebra fish", "Danio rerio","Arabidopsis thaliana","Rice", "Oryza sativa","Sea Squirt", "Ciona intestinalis","Barley", "Hordeum vulgare","Frog", "Xenopus tropicalis","Soybean", "Glycine max","Fruit fly", "Drosophila melanogaster","Horse", "Equus caballus", "Rhesus Monkey", "Macaca mulatta","Wine Grape", "Vitis vinifera", "Yeast", "Saccharomyces cerevisiae", "Tomato", "Solanum lycopersicum", "Rat", "Rattus norvegicus", "Cow", "Bos taurus", "Western Balsam Poplar", "Populus trichocarpa", "Chimpanzee", "Pan troglodytes","Indian Rice", "Oryza indica","Dog", "Canis familiaris", "Maize", "Zea mays","Pig", "Sus scrofa","Worm", "Caenorhabditis elegans", "Platypus", "Ornithorhynchus anatinus", "Chicken", "Gallus gallus", "Fusarium graminearum", "Gibberella zeae","Bacillus subtilis", "Escherichia coli", "Black mold", "Aspergillus niger", "Mouse", "Mus musculus"] - }, - "x-orn:returns":{ - "x-orn-@id": "x-orn:Identifier", - "x-orn-@type": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - }, - "tags":["Genes","Metabolites","Chemicals","Proteins"], - "parameters": [ - { - "name": "dataSource", - "x-orn-@id": "x-orn:dataSource", - "in": "query", - "x-orn-@type": ["x-orn:Descriptor","string"], - "x-orn:expects": { - "x-orn-@id": "x-orn:Identifier", - "x-orn-@type": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - }, - "description": "(Optional) Restrict results by data source [system code](https://bridgedb.github.io/pages/system-codes.html)", - "required": false, - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] -}, - { - "name": "organism", - "x-orn-@id": "x-orn:organism", - "in": "path", - "x-orn-@type": ["x-orn:taxonomy","string"], - "x-orn:expects": { - "x-orn-@id": "x-orn:taxonomy", - "x-orn-@type": ["Human", "Homo sapiens","Tuberculosis", "Mycobacterium tuberculosis","Mosquito", "Anopheles gambiae","Zebra fish", "Danio rerio","Arabidopsis thaliana","Rice", "Oryza sativa","Sea Squirt", "Ciona intestinalis","Barley", "Hordeum vulgare","Frog", "Xenopus tropicalis","Soybean", "Glycine max","Fruit fly", "Drosophila melanogaster","Horse", "Equus caballus", "Rhesus Monkey", "Macaca mulatta","Wine Grape", "Vitis vinifera", "Yeast", "Saccharomyces cerevisiae", "Tomato", "Solanum lycopersicum", "Rat", "Rattus norvegicus", "Cow", "Bos taurus", "Western Balsam Poplar", "Populus trichocarpa", "Chimpanzee", "Pan troglodytes","Indian Rice", "Oryza indica","Dog", "Canis familiaris", "Maize", "Zea mays","Pig", "Sus scrofa","Worm", "Caenorhabditis elegans", "Platypus", "Ornithorhynchus anatinus", "Chicken", "Gallus gallus", "Fusarium graminearum", "Gibberella zeae","Bacillus subtilis", "Escherichia coli", "Black mold", "Aspergillus niger", "Mouse", "Mus musculus"] - }, - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "enum": ["Human", "Homo sapiens","Tuberculosis", "Mycobacterium tuberculosis","Mosquito", "Anopheles gambiae","Zebra fish", "Danio rerio","Arabidopsis thaliana","Rice", "Oryza sativa","Sea Squirt", "Ciona intestinalis","Barley", "Hordeum vulgare","Frog", "Xenopus tropicalis","Soybean", "Glycine max","Fruit fly", "Drosophila melanogaster","Horse", "Equus caballus", "Rhesus Monkey", "Macaca mulatta","Wine Grape", "Vitis vinifera", "Yeast", "Saccharomyces cerevisiae", "Tomato", "Solanum lycopersicum", "Rat", "Rattus norvegicus", "Cow", "Bos taurus", "Western Balsam Poplar", "Populus trichocarpa", "Chimpanzee", "Pan troglodytes","Indian Rice", "Oryza indica","Dog", "Canis familiaris", "Maize", "Zea mays","Pig", "Sus scrofa","Worm", "Caenorhabditis elegans", "Platypus", "Ornithorhynchus anatinus", "Chicken", "Gallus gallus", "Fusarium graminearum", "Gibberella zeae","Bacillus subtilis", "Escherichia coli", "Black mold", "Aspergillus niger", "Mouse", "Mus musculus"] - }, - { - "name": "systemCode", - "in": "path", - "x-orn-@type": ["x-orn:Descriptor","string"], - "description": "Source (input) data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": true, - "default": "L", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - }, - { - "name": "identifier", - "x-orn-@type": ["x-orn:Descriptor","string"], - "x-orn-@id": "x-orn:Identifier", - "x-orn:expects": "x-orn:Identifier", - "in": "path", - "description": "Identifier", - "required": true, - "default": "1234" - } - ], - "responses": { - "200": { - "x-orn:returns": "Returns a tab-delimited list of xrefs that map to a given identifier", - "description": "Returns a tab-delimited list of xrefs that map to a given identifier" - } - } - } - }, - -"/{organism}/xrefsBatch/{systemCode}": { - "post": { - "description": "Returns a list of xrefs, that maps to a given list of identifiers to a given data source and organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "dataSource", - "in": "query", - "description": "(Optional) Restrict results by data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": false, - "type": "string", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - - }, - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "systemCode", - "in": "path", - "description": "Source (input) data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": true, - "type": "string", - "default": "L", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - }, - { - "in": "body", - "name": "body", - "description": "List of identifiers. The separator is a new line (\\n)", - "required": true, - "schema": { - "type": "string", - "example": "ENSMUSG00000063455\nENSMUSG00000073823\nENSMUSG00000037031" - } - } - ], - "responses": { - "200": { - "description": "Returns a tab-delimited list of xrefs that map to a given identifier" - } - } - } - }, - "/{organism}/xrefsBatch": { - "post": { - "description": "Returns a list of xrefs, per identifier, that maps to a given list of identifiers an data source given an organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "dataSource", - "in": "query", - "description": "(Optional) Restrict results by data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": false, - "type": "string", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - - }, - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "in": "body", - "name": "body", - "description": "List of tab separated values: idsystemcode\\n", - "required": true, - "schema":{ - "example": "17716\tL\n17717\tL\nENSMUSG00000032462\tEn\nENSMUSG00000021938\tEn", - "format" : "string", - "type" : "string" - } - } - ], - "responses": { - "200": { - "description": "Returns a tab-delimited list of xrefs that map to a given identifier" - } - } - } - }, - "/{organ­ism}/xrefs/{systemCode}/{identifier}": { - "get": { - "description": "Returns a list of xrefs that map to a given identifier, and data source. Optionally restrict results to a given data source.", - "tags":["Metabolites"], - "parameters": [ - { - "name": "dataSource", - "in": "query", - "description": "(Optional) Restrict results by data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": false, - "type": "string" - }, - { - "name": "organ­ism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName). Note: despite the presence of this parameter, this endpoint returns the same results regardless of organism specified.", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "systemCode", - "in": "path", - "description": "Source (input) data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": true, - "type": "string", - "default": "Ce", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - }, - { - "name": "identifier", - "in": "path", - "description": "system", - "required": true, - "type": "string", - "default": "CHEBI:29108" - } - ], - "responses": { - "200": { - "description": "Successful response" - } - } - } - }, - - "/{organism}/xrefExists/{systemCode}/{identifier}": { - "get": { - "description": "Returns `true` or `false` based on whether or not an xref exists in the database given an identifier, data source, and organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "systemCode", - "in": "path", - "description": "Source (input) data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": true, - "type": "string", - "default": "L", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - - }, - { - "name": "identifier", - "in": "path", - "description": "Identifier", - "required": true, - "default":"1234", - "type": "string" - - } - ], - "responses": { - "200": { - "description": "Returns `true` or `false`" - } - } - } - }, - "/{organism}/search/{query}": { - "get": { - "description": "Returns a list of xrefs with identifiers that contain the query string for a given organism. Results are not restricted to exact matches. Optionally limit results to a specified number per data source.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "query", - "in": "path", - "description": "Identifier query", - "required": true, - "type": "string", - "default":"1234" - }, - { - "name": "limit", - "in": "query", - "description": "Number of results per data source", - "required": false, - "type": "integer" - } - ], - "responses": { - "200": { - "description": "Returns a tab-delimited list of xrefs with identifiers that contain the query string for a given organism" - } - } - } - }, - "/{organism}/properties": { - "get": { - "description": "Returns the list of properties available for a given organism\n", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - } - ], - "responses": { - "200": { - "description": "Returns the list of properties available for a given organism" - } - } - } - }, - "/{organism}/sourceDataSources": { - "get": { - "description": "Returns a list of data sources available as xref sources for a given organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - } - ], - "responses": { - "200": { - "description": "Returns a list of data sources available as xref sources." - } - } - } - }, - "/{organism}/targetDataSources": { - "get": { - "description": "Returns a list of data sources available as xref targets for a given organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - } - ], - "responses": { - "200": { - "description": "Returns a list of data sources available as xref targets." - } - } - } - }, - "/{organism}/isFreeSearchSupported": { - "get": { - "description": "Returns `true` or `false` based on whether or not /{organism}/search/{query} is supported for a given organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - } - ], - "responses": { - "200": { - "description": "Returns `true` or `false`." - } - } - } - }, - "/{organism}/isMappingSupported/{sourceSystemCode}/{targetSystemCode}": { - "get": { - "description": "Returns `true` or `false` based on whether or not /{organism}/xrefs/{systemCode}/{identifier} would possibly return a {targetSystemCode} result given a {sourceSystemCode} query. This function basically combines the results of /{organism}/sourceDataSources and /{organism}/targetDataSources into a single boolean result.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "sourceSystemCode", - "in": "path", - "description": "[System code](http://vocabularies.bridgedb.org/#systemCode) for source (input/query) data source", - "required": true, - "type": "string", - "default": "L", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - - }, - { - "name": "targetSystemCode", - "in": "path", - "description": "[System code](http://vocabularies.bridgedb.org/#systemCode) for target (output/result) data source", - "required": true, - "type": "string", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - } - ], - "responses": { - "200": { - "description": "Returns `true` or `false`." - } - } - } - }, - "/{organism}/attributeSearch/{query}": { - "get": { - "description": "Returns a list of xrefs and associated attributes that contain the query string for a given organism. Results are not restricted to exact matches. Optionally limit results to a specified number per data source, or by the type of attribute. See possible attribute types via /{organism}/attributeSet.\n", - "tags":["Genes","Metabolites"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "query", - "in": "path", - "description": "Text to find in attributes", - "required": true, - "type": "string" - }, - { - "name": "limit", - "in": "query", - "description": "Number of results", - "required": false, - "type": "integer" - }, - { - "name": "attrName", - "in": "query", - "description": "Restrict search by attribute name (case sensitive). Use GET /{organism}/attributeSet to find out which attributes are supported.", - "required": false, - "type": "string" - } - ], - "responses": { - "200": { - "description": "returns a tab-delimited list with the identifier, data source and descriptions found." - } - } - } - }, - "/{organism}/attributes/{systemCode}/{identifier}": { - "get": { - "description": "Returns the attributes for a given identifier, data source, organism. Optionally display only a specified attribute", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "systemCode", - "in": "path", - "description": "System", - "required": true, - "type": "string", - "default" : "En", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - }, - { - "name": "identifier", - "in": "path", - "description": "Identifier", - "required": true, - "type": "string", - "default": "ENSG00000122375" - }, - { - "name": "attrName", - "in": "query", - "description": "Type of attribute", - "required": false, - "type": "string" - } - ], - "responses": { - "200": { - "description": "Returns a tab-delimited list with the attributes and their content" - } - } - } - }, - "/{organism}/attributeSet": { - "get": { - "description": "Returns the supported attributes to the given Organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - } - ], - "responses": { - "200": { - "description": "Returns the supported attributes" - } - } - } - } - - - - -}, -"@context": { - "@vocab": "http://openrisknet.org/schema#", - "x-orn": "http://openrisknet.org/schema#", - "x-orn-@id": "@id", - "x-orn-@type":"@type", - "title": "x-orn:title", - "info": "x-orn:info", - "paths": - { "@id": "x-orn:paths" - }, - "Ik": "http://semanticscience.org/resource/CHEMINF_000059", - "En":"http://edamontology.org/data_1033", - "Cs":"http://semanticscience.org/resource/CHEMINF_000405", - "Ck":"http://semanticscience.org/resource/CHEMINF_000409", - "Ch":"http://semanticscience.org/resource/CHEMINF_000408", - "Pd":"http://semanticscience.org/resource/CHEMINF_000408", - "U":"http://edamontology.org/data_1104", - "Ma":"http://edamontology.org/data_2641", - "Lm":"http://semanticscience.org/resource/CHEMINF_000564", - "Wd":"http://semanticscience.org/resource/CHEMINF_000567", - "Cpc":"http://semanticscience.org/resource/CHEMINF_000140", - "Rk":"http://edamontology.org/data_2608", - "Ce":"http://semanticscience.org/resource/CHEMINF_000407", - "S":"http://edamontology.org/data_3021", - "L":"http://edamontology.org/data_1027", - "Om":"http://edamontology.org/data_1153", - "T":"http://edamontology.org/data_1176", - "H":"http://edamontology.org/data_2298", - "Re":"http://edamontology.org/data_1155", - "Q":"http://edamontology.org/data_1098", - "Ca":"http://semanticscience.org/resource/CHEMINF_000446", - "Up":"http://edamontology.org/data_2645", - "organism":"http://purl.bioontology.org/ontology/NCBITAXON/131567", - "Human":"http://purl.bioontology.org/ontology/NCBITAXON/9606", -"Homo sapiens":"http://purl.bioontology.org/ontology/NCBITAXON/9606", -"Tuberculosis":"http://purl.bioontology.org/ontology/NCBITAXON/1773", -"Mycobacterium tuberculosis":"http://purl.bioontology.org/ontology/NCBITAXON/1773", -"Mosquito":"http://purl.bioontology.org/ontology/NCBITAXON/7165", -"Anopheles gambiae":"http://purl.bioontology.org/ontology/NCBITAXON/7165", -"Zebra fish":"http://purl.bioontology.org/ontology/NCBITAXON/7955", -"Danio rerio":"http://purl.bioontology.org/ontology/NCBITAXON/7955", -"Arabidopsis thaliana":"http://purl.bioontology.org/ontology/NCBITAXON/3702", -"Rice":"http://purl.bioontology.org/ontology/NCBITAXON/4530", -"Oryza sativa":"http://purl.bioontology.org/ontology/NCBITAXON/4530", -"Sea Squirt":"http://purl.bioontology.org/ontology/NCBITAXON/7719", -"Ciona intestinalis":"http://purl.bioontology.org/ontology/NCBITAXON/7719", -"Barley":"http://purl.bioontology.org/ontology/NCBITAXON/4513", -"Hordeum vulgare":"http://purl.bioontology.org/ontology/NCBITAXON/4513", -"Frog":"http://purl.bioontology.org/ontology/NCBITAXON/8364", -"Xenopus tropicalis":"http://purl.bioontology.org/ontology/NCBITAXON/8364", -"Soybean":"http://purl.bioontology.org/ontology/NCBITAXON/3847", -"Glycine max":"http://purl.bioontology.org/ontology/NCBITAXON/3847", -"Fruit fly":"http://purl.bioontology.org/ontology/NCBITAXON/7227", -"Drosophila melanogaster":"http://purl.bioontology.org/ontology/NCBITAXON/7227", -"Horse":"http://purl.bioontology.org/ontology/NCBITAXON/9796", -"Equus caballus":"http://purl.bioontology.org/ontology/NCBITAXON/9796", -"Rhesus Monkey":"http://purl.bioontology.org/ontology/NCBITAXON/9544", -"Macaca mulatta":"http://purl.bioontology.org/ontology/NCBITAXON/9544", -"Wine Grape":"http://purl.bioontology.org/ontology/NCBITAXON/29760", -"Vitis vinifera":"http://purl.bioontology.org/ontology/NCBITAXON/29760", -"Yeast":"http://purl.bioontology.org/ontology/NCBITAXON/4932", -"Saccharomyces cerevisiae":"http://purl.bioontology.org/ontology/NCBITAXON/4932", -"Tomato":"http://purl.bioontology.org/ontology/NCBITAXON/4081", -"Solanum lycopersicum":"http://purl.bioontology.org/ontology/NCBITAXON/4081", -"Rat":"http://purl.bioontology.org/ontology/NCBITAXON/10116", -"Rattus norvegicus":"http://purl.bioontology.org/ontology/NCBITAXON/10116", -"Cow":"http://purl.bioontology.org/ontology/NCBITAXON/9913", -"Bos taurus":"http://purl.bioontology.org/ontology/NCBITAXON/9913", -"Western Balsam Poplar":"http://purl.bioontology.org/ontology/NCBITAXON/3694", -"Populus trichocarpa":"http://purl.bioontology.org/ontology/NCBITAXON/3694", -"Chimpanzee":"http://purl.bioontology.org/ontology/NCBITAXON/9598", -"Pan troglodytes":"http://purl.bioontology.org/ontology/NCBITAXON/9598", -"Maize":"http://purl.bioontology.org/ontology/NCBITAXON/4577", -"Zea mays":"http://purl.bioontology.org/ontology/NCBITAXON/4577", -"Pig":"http://purl.bioontology.org/ontology/NCBITAXON/9823", -"Sus scrofa":"http://purl.bioontology.org/ontology/NCBITAXON/9823", -"Worm":"http://purl.bioontology.org/ontology/NCBITAXON/6239", -"Caenorhabditis elegans":"http://purl.bioontology.org/ontology/NCBITAXON/6239", -"Platypus":"http://purl.bioontology.org/ontology/NCBITAXON/9258", -"Ornithorhynchus anatinus":"http://purl.bioontology.org/ontology/NCBITAXON/9258", -"Chicken":"http://purl.bioontology.org/ontology/NCBITAXON/9031", -"Gallus gallus":"http://purl.bioontology.org/ontology/NCBITAXON/9031", -"Fusarium graminearum":"http://purl.bioontology.org/ontology/NCBITAXON/5518", -"Gibberella zeae":"http://purl.bioontology.org/ontology/NCBITAXON/5518", -"Bacillus subtilis":"http://purl.bioontology.org/ontology/NCBITAXON/1423", -"Escherichia coli":"http://purl.bioontology.org/ontology/NCBITAXON/562", -"Black mold":"http://purl.bioontology.org/ontology/NCBITAXON/5061", -"Aspergillus niger":"http://purl.bioontology.org/ontology/NCBITAXON/5061", -"Mouse":"http://purl.bioontology.org/ontology/NCBITAXON/10090", -"Mus musculus":"http://purl.bioontology.org/ontology/NCBITAXON/10090" -} -} diff --git a/swagger-ui b/swagger-ui deleted file mode 160000 index ccf17e9..0000000 --- a/swagger-ui +++ /dev/null @@ -1 +0,0 @@ -Subproject commit ccf17e90e2059ef94b152253727ea66178f907df diff --git a/swagger.json b/swagger.json deleted file mode 100644 index f380152..0000000 --- a/swagger.json +++ /dev/null @@ -1,942 +0,0 @@ -{ - "swagger": "2.0", - "info": { - "version": "0.9.0", - "title": "bridgedb webservices" - }, - "consumes":["text/html"], - "produces":["*/*"], - "host": "", - "schemes": [ - "http" - ], - "paths": { - "/{organism}/xrefs/{systemCode}/{identifier}": { - "get": { - "description": "Returns a list of xrefs that map to a given identifier, data source, and organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "dataSource", - "in": "query", - "description": "(Optional) Restrict results by data source [system code](https://bridgedb.github.io/pages/system-codes.html)", - "required": false, - "type": "string", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - - }, - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Mouse", "Mus musculus", - "Rat", "Rattus norvegicus", - "Zebra fish", "Danio rerio", - "Fruit fly", "Drosophila melanogaster", - "Worm", "Caenorhabditis elegans", - "Daphnia magna", "Daphnia pulex", - "Escherichia coli", - "Chicken", "Gallus gallus", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Platypus", "Ornithorhynchus anatinus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Black mold", "Aspergillus niger" - ] - }, - { - "name": "systemCode", - "in": "path", - "description": "Source (input) data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": true, - "type": "string", - "default": "L", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - }, - { - "name": "identifier", - "in": "path", - "description": "Identifier", - "required": true, - "type": "string", - "default": "1234" - } - ], - "responses": { - "200": { - "description": "Returns a tab-delimited list of xrefs that map to a given identifier" - } - } - } - }, - "/{organism}/xrefsBatch/{systemCode}": { - "post": { - "description": "Returns a list of xrefs, that maps to a given list of identifiers to a given data source and organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "dataSource", - "in": "query", - "description": "(Optional) Restrict results by data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": false, - "type": "string", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - - }, - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "systemCode", - "in": "path", - "description": "Source (input) data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": true, - "type": "string", - "default": "L", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - }, - { - "in": "body", - "name": "body", - "description": "List of identifiers. The separator is a new line (\\n)", - "required": true, - "schema": { - "type": "string", - "example": "ENSMUSG00000063455\nENSMUSG00000073823\nENSMUSG00000037031" - } - } - ], - "responses": { - "200": { - "description": "Returns a tab-delimited list of xrefs that map to a given identifier" - } - } - } - }, - "/{organism}/xrefsBatch": { - "post": { - "description": "Returns a list of xrefs, per identifier, that maps to a given list of identifiers an data source given an organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "dataSource", - "in": "query", - "description": "(Optional) Restrict results by data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": false, - "type": "string", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - - }, - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "in": "body", - "name": "body", - "description": "List of tab separated values: idsystemcode\\n", - "required": true, - "schema":{ - "example": "17716\tL\n17717\tL\nENSMUSG00000032462\tEn\nENSMUSG00000021938\tEn", - "format" : "string", - "type" : "string" - } - } - ], - "responses": { - "200": { - "description": "Returns a tab-delimited list of xrefs that map to a given identifier" - } - } - } - }, - "/{organ­ism}/xrefs/{systemCode}/{identifier}": { - "get": { - "description": "Returns a list of xrefs that map to a given identifier, and data source. Optionally restrict results to a given data source.", - "tags":["Metabolites"], - "parameters": [ - { - "name": "dataSource", - "in": "query", - "description": "(Optional) Restrict results by data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": false, - "type": "string" - }, - { - "name": "organ­ism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName). Note: despite the presence of this parameter, this endpoint returns the same results regardless of organism specified.", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "systemCode", - "in": "path", - "description": "Source (input) data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": true, - "type": "string", - "default": "Ce", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - }, - { - "name": "identifier", - "in": "path", - "description": "system", - "required": true, - "type": "string", - "default": "CHEBI:29108" - } - ], - "responses": { - "200": { - "description": "Successful response" - } - } - } - }, - - "/{organism}/xrefExists/{systemCode}/{identifier}": { - "get": { - "description": "Returns `true` or `false` based on whether or not an xref exists in the database given an identifier, data source, and organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "systemCode", - "in": "path", - "description": "Source (input) data source [system code](http://vocabularies.bridgedb.org/#systemCode)", - "required": true, - "type": "string", - "default": "L", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - - }, - { - "name": "identifier", - "in": "path", - "description": "Identifier", - "required": true, - "default":"1234", - "type": "string" - - } - ], - "responses": { - "200": { - "description": "Returns `true` or `false`" - } - } - } - }, - "/{organism}/search/{query}": { - "get": { - "description": "Returns a list of xrefs with identifiers that contain the query string for a given organism. Results are not restricted to exact matches. Optionally limit results to a specified number per data source.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "query", - "in": "path", - "description": "Identifier query", - "required": true, - "type": "string", - "default":"1234" - }, - { - "name": "limit", - "in": "query", - "description": "Number of results per data source", - "required": false, - "type": "integer" - } - ], - "responses": { - "200": { - "description": "Returns a tab-delimited list of xrefs with identifiers that contain the query string for a given organism" - } - } - } - }, - "/{organism}/properties": { - "get": { - "description": "Returns the list of properties available for a given organism\n", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - } - ], - "responses": { - "200": { - "description": "Returns the list of properties available for a given organism" - } - } - } - }, - "/{organism}/sourceDataSources": { - "get": { - "description": "Returns a list of data sources available as xref sources for a given organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - } - ], - "responses": { - "200": { - "description": "Returns a list of data sources available as xref sources." - } - } - } - }, - "/{organism}/targetDataSources": { - "get": { - "description": "Returns a list of data sources available as xref targets for a given organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - } - ], - "responses": { - "200": { - "description": "Returns a list of data sources available as xref targets." - } - } - } - }, - "/{organism}/isFreeSearchSupported": { - "get": { - "description": "Returns `true` or `false` based on whether or not /{organism}/search/{query} is supported for a given organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - } - ], - "responses": { - "200": { - "description": "Returns `true` or `false`." - } - } - } - }, - "/{organism}/isMappingSupported/{sourceSystemCode}/{targetSystemCode}": { - "get": { - "description": "Returns `true` or `false` based on whether or not /{organism}/xrefs/{systemCode}/{identifier} would possibly return a {targetSystemCode} result given a {sourceSystemCode} query. This function basically combines the results of /{organism}/sourceDataSources and /{organism}/targetDataSources into a single boolean result.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "sourceSystemCode", - "in": "path", - "description": "[System code](http://vocabularies.bridgedb.org/#systemCode) for source (input/query) data source", - "required": true, - "type": "string", - "default": "L", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - - }, - { - "name": "targetSystemCode", - "in": "path", - "description": "[System code](http://vocabularies.bridgedb.org/#systemCode) for target (output/result) data source", - "required": true, - "type": "string", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - } - ], - "responses": { - "200": { - "description": "Returns `true` or `false`." - } - } - } - }, - "/{organism}/attributeSearch/{query}": { - "get": { - "description": "Returns a list of xrefs and associated attributes that contain the query string for a given organism. Results are not restricted to exact matches. Optionally limit results to a specified number per data source, or by the type of attribute. See possible attribute types via /{organism}/attributeSet.\n", - "tags":["Genes","Metabolites"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "query", - "in": "path", - "description": "Text to find in attributes", - "required": true, - "type": "string" - }, - { - "name": "limit", - "in": "query", - "description": "Number of results", - "required": false, - "type": "integer" - }, - { - "name": "attrName", - "in": "query", - "description": "Restrict search by attribute name (case sensitive). Use GET /{organism}/attributeSet to find out which attributes are supported.", - "required": false, - "type": "string" - } - ], - "responses": { - "200": { - "description": "returns a tab-delimited list with the identifier, data source and descriptions found." - } - } - } - }, - "/{organism}/attributes/{systemCode}/{identifier}": { - "get": { - "description": "Returns the attributes for a given identifier, data source, organism. Optionally display only a specified attribute", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - }, - { - "name": "systemCode", - "in": "path", - "description": "System", - "required": true, - "type": "string", - "default" : "En", - "enum": ["En","Cs","X","E","Rh","Ck","Eco","Cg","Ch","Il","Uc","Rf","Pd","U","Ma","Lm","Wd","Wi","Cpc","Mb","Rk","Ce","S","L","Wg","Om","T","Mc","Ik","H", "Re", "Ag", "Q", "Ca", "Up","Cks"] - }, - { - "name": "identifier", - "in": "path", - "description": "Identifier", - "required": true, - "type": "string", - "default": "ENSG00000122375" - }, - { - "name": "attrName", - "in": "query", - "description": "Type of attribute", - "required": false, - "type": "string" - } - ], - "responses": { - "200": { - "description": "Returns a tab-delimited list with the attributes and their content" - } - } - } - }, - "/{organism}/attributeSet": { - "get": { - "description": "Returns the supported attributes to the given Organism.", - "tags":["Genes"], - "parameters": [ - { - "name": "organism", - "in": "path", - "description": "Organism [Latin name](http://vocabularies.bridgedb.org/#latinName) or [short name](http://vocabularies.bridgedb.org/#shortName).", - "required": true, - "type": "string", - "enum": ["Human", "Homo sapiens", - "Tuberculosis", "Mycobacterium tuberculosis", - "Mosquito", "Anopheles gambiae", - "Zebra fish", "Danio rerio", - "Arabidopsis thaliana", - "Rice", "Oryza sativa", - "Sea Squirt", "Ciona intestinalis", - "Barley", "Hordeum vulgare", - "Frog", "Xenopus tropicalis", - "Soybean", "Glycine max", - "Fruit fly", "Drosophila melanogaster", - "Horse", "Equus caballus", - "Rhesus Monkey", "Macaca mulatta", - "Wine Grape", "Vitis vinifera", - "Yeast", "Saccharomyces cerevisiae", - "Tomato", "Solanum lycopersicum", - "Rat", "Rattus norvegicus", - "Cow", "Bos taurus", - "Western Balsam Poplar", "Populus trichocarpa", - "Chimpanzee", "Pan troglodytes", - "Indian Rice", "Oryza indica", - "Dog", "Canis familiaris", - "Maize", "Zea mays", - "Pig", "Sus scrofa", - "Worm", "Caenorhabditis elegans", - "Platypus", "Ornithorhynchus anatinus", - "Chicken", "Gallus gallus", - "Fusarium graminearum", "Gibberella zeae", - "Bacillus subtilis", - "Escherichia coli", - "Black mold", "Aspergillus niger", - "Mouse", "Mus musculus"] - } - ], - "responses": { - "200": { - "description": "Returns the supported attributes" - } - } - } - } - } - -} diff --git a/v3/index.css b/v3/index.css deleted file mode 100644 index f2376fd..0000000 --- a/v3/index.css +++ /dev/null @@ -1,16 +0,0 @@ -html { - box-sizing: border-box; - overflow: -moz-scrollbars-vertical; - overflow-y: scroll; -} - -*, -*:before, -*:after { - box-sizing: inherit; -} - -body { - margin: 0; - background: #fafafa; -} diff --git a/v3/index.html b/v3/index.html deleted file mode 100644 index 6469f3b..0000000 --- a/v3/index.html +++ /dev/null @@ -1,43 +0,0 @@ - - - - - - Swagger UI - - - - - - - - - -
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