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19
datasets available to search
ShareScore release 0.7.1
Dataset results
19 results for “BridgeDb”
Gene/Protein BridgeDb ID Mapping Database (Ensembl Fungi 49)
<p>Ensembl Fungi 49 derived ID mapping database for use with BridgeDb.<br> The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 103)
<p>Ensembl 103 derived ID mapping database for use with BridgeDb.</p> <p><br> This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 104)
<p>Ensembl 104 derived ID mapping database for use with BridgeDb.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 105)
<p>Ensembl 105 derived ID mapping databases for use with BridgeDb.</p> <p>The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl Metazoa 49)
<p>Ensembl Metazoa 49 derived ID mapping databases for use with BridgeDb.<br> The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).<br> </p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl Plants 49)
<p>Ensembl Plants 49 derived ID mapping database for use with BridgeDb.<br> The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl Metazoa 52)
<p>Mapping databases derived from Ensembl Metazoa 52. These files can be used with BridgeDb.<br> The scripts which were used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 85)
<p>Ensembl 85 derived ID mapping database for use with <a href="https://bridgedb.github.io/">BridgeDb</a> and was created with <a href="https://github.com/bridgedb/create-bridgedb-genedb">custom code</a>.</p>
BridgeDb: Human and SARS-related corona virus gene/protein mapping database derived from Wikidata
<p>Gene/Protein mappings for human and SARS-related coronaviruses. Data is derived from Wikidata. Mappings from Wikidata to NCBI Gene, RefSeq, UniProt, and Guide to Pharmacology Target are provided in the .bridge file.</p> <ul> <li>179 Wikidata (Wd) identifiers</li> <li>82 Uniprot-TrEMBL (S) identifiers</li> <li>70 NCBI Gene (L) identifiers</li> <li>66 RefSeq (Q) identifiers</li> <li>9 Guide to Pharmacology Target (Gpt) identifiers</li> </ul> <p>Virus name was added as attribute ("virus") to Wikidata Xrefs.</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl Fungi 52)
<p>Mapping databases derived from Ensembl Fungi 52. These files can be used with BridgeDb.<br> This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio).</p> <p>The scripts which were used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 106)
<p>Ensembl 106 derived ID mapping databases for use with BridgeDb.<br> This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio).</p> <p>The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl Plants 52)
<p>Mapping databases derived from Ensembl Plants 52. These files can be used with BridgeDb.<br> This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio).</p> <p>The scripts which were used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 107)
<p>Ensembl 107 derived ID mapping databases for use with BridgeDb.<br> This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio).</p> <p>The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p> </p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 108)
<p>Ensembl 108 derived ID mapping databases for use with BridgeDb.<br> <br> The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p>
BridgeDb: pathway identifier mapping database derived from Wikidata
<p>First release of a BridgeDb pathway identifier mapping database. Currently supports Wikidata and WikiPathways identifiers. CCZero.</p> <pre><code>[INFO]: Database finished. INFO: old database is Wikidata 1.0.0 (build: 20211211) INFO: new database is Wikidata 1.0.0 (build: 20211211) INFO: Number of ids in Wd (Wikidata): 905 (unchanged) INFO: Number of ids in Wp (WikiPathways): 900 (unchanged) INFO: new size is 2 Mb (changed +0.0%) INFO: total number of identifiers is 1805 INFO: total number of mappings is 1810 </code></pre> <p> </p>
BridgeDb Complex Identifier Mapping Database
<p>BridgeDb identifier mapping databases for complexes extracted from Wikidata. Code to generate the database (https://github.com/bridgedb/Wikidata2Bridgedb - ComplexIdentifiers.java). </p>
WikiPathways WPRDF BridgeDb ID mapping triples
<p>Created from the Nightly WPRDF data from 2023-03-31 by loading the RDF into a local Blazegraph instance and running the below query and exporting this as `.ttl` file:</p> <p>```sparql</p> <p>PREFIX bdb: <http://vocabularies.wikipathways.org/wp#bdb></p> <p>CONSTRUCT { ?s ?p ?o } WHERE {<br> VALUES ?p {<br> bdb:Wikidata bdb:Ensembl bdb:Uniprot bdb:EntrezGene<br> bdb:ChEBI bdb:Chemspider bdb:ComplexPortal bdb:HgncSymbol<br> bdb:Hmdb bdb:InChIKey bdb:KeggCompound bdb:LipidMaps<br> bdb:PubChem bdb:Rhea bdb:Uniprot bdb:Reactome<br> }<br> ?s ?p ?o .<br> }</p> <p>```</p>
BridgeDb: pathway identifier mapping database derived from Wikidata
<p>Release of a BridgeDb gene identifier mapping database between Wikidata and Ensembl.</p> <pre>[INFO]: Database finished. INFO: old database is Wikidata 1.0.0 (build: 20230506) INFO: new database is Wikidata 1.0.0 (build: 20230506) INFO: Number of ids in Wd (Wikidata): 153715 (unchanged) INFO: Number of ids in En (Ensembl): 153637 (unchanged) INFO: new size is 95 Mb (changed +0.0%) INFO: total number of identifiers is 307352 INFO: total number of mappings is 307430 </pre>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 91)
<p>Ensembl 91 derived ID mapping database for use with BridgeDb.</p>
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