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The table below lists the types of annotations and the corresponding providers.</p> <table> <tbody> <tr> <td style="width: 200px;"></td> <td style="background-color: #D5EACB;"><strong>Named Entities</strong> (Accessions, Genes/Proteins, Chemicals, Organisms, Diseases, Gene Ontology, Resources, Experimental Methods)</td> <td style="background-color: #D5EACB;"><strong>Gene Mutations</strong></td> <td style="background-color: #D5EACB;"><strong>Gene-Disease relationships</strong></td> <td style="background-color: #D5EACB;"><strong>Gene Functional annotations, COVoc accession numbers</strong></td> <td style="background-color: #D5EACB;"><strong>Protein-protein interaction</strong></td> <td style="background-color: #D5EACB;"><strong>Transcription factor - Target gene relationships</strong></td> <td style="background-color: #D5EACB;"><strong>Biological event</strong> (Phosphosrylation events)</td> <td style="background-color: #D5EACB;"><strong>Cells, Cell Lines, Clinical Drugs, Sequences, Molecular Processes, Organ Tissues</strong></td> <td style="background-color: #D5EACB;"><strong>Cells, Phenotypes, Molecules, Anatomy, Pathways</strong></td> <td style="background-color: #D5EACB;"><strong>Sample-Material, Body-Site, Host, State, Site, Place, Date, Engineered, Ecoregion, Treatment, Kit, Primer, Gene, LS, LCM, Sequencing</strong></td> </tr> <tr> <td class="provider_name_table"><a href=" https://www.europepmc.org" target="_blank">Europe PMC</a></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> </tr> <tr> <td class="provider_name_table"><a href=" https://www.sib.swiss/patrick-ruch-group" target="_blank">HES-SO/SIB</a></td> <td></td> <td></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> </tr> <tr> <td class="provider_name_table"><a href="http://www.disgenet.org/" target="_blank">DisGeNET</a></td> <td></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> </tr> <tr> <td class="provider_name_table"><a href="https://www.targetvalidation.org/" target="_blank">Open Targets Platform</a></td> <td></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> </tr> <tr> <td class="provider_name_table"><a href="https://www.ebi.ac.uk/intact/" target="_blank">IntAct</a></td> <td></td> <td></td> <td></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> <td></td> <td></td> <td></td> <td></td> </tr> <tr> <td class="provider_name_table"><a href="http://www.nactem.ac.uk/" target="_blank">NaCTEM</a></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> <td></td> <td></td> </tr> <tr> <td class="provider_name_table"><a href="https://www.ncbi.nlm.nih.gov/research/pubtator" target="_blank">PubTator (NCBI)</a></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> </tr> <tr> <td class="provider_name_table"><a href="https://www.extri.org/" target="_blank">ExTRI(NTNU/CNIO/BSC)</a></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> <td></td> <td></td> <td></td> </tr> <tr> <td class="provider_name_table"><a href="http://www.ontogene.org/" target="_blank">OntoGene</a></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> <td></td> </tr> <tr> <td class="provider_name_table"><a href="https://sites.google.com/site/nhcollier/projects/phenebank" target="_blank">PheneBank</a></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> <td></td> </tr> <tr> <td class="provider_name_table"><a href="https://gtr.ukri.org/projects?ref=BB%2FS009043%2F1" target="_blank">Metagenomics (EMERALD)</a></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td></td> <td style="text-align:center"><i class="fa fa-check" aria-hidden="true"></i></td> </tr> </tbody> </table> <p>If you are a text-mining group and can supply annotations in the format we require read <a href="/AnnotationsSubmission">here</a></p> </div> <div id="jsonLD"> <h3>JSON-LD Annotations format</h3> <p> This paragraph describes details on providing annotations data as JSON-LD. JSON-LD (JSON for Linking Data) is a variant of JSON that enables linking data from different resources. For more details on JSON-LD refer to the following links: <a href="https://json-ld.org/" target="_blank">JSON-LD definition</a> and <a href="https://json-ld.org/spec/ED/json-ld-syntax/20111016/" target="_blank">JSON-LD syntax</a>.</p> <p> The annotations are modelled in the Web Annotations Data Model (OA). For more details on the OA model, refer to the following links: <a href="https://www.w3.org/TR/annotation-model/" target="_blank">OA definition</a> and <a href="https://www.w3.org/TR/annotation-vocab/" target="_blank">OA vocabulary</a>. </p> <p> To represent annotations as JSON-LD a context must be provided (represented by the keyword @context in JSON-LD). The context allows applications to interpret the data being exchanged (using a set of URIs linking to various terms in specified vocabularies and ontologies). For the the purpose of Annotation API, the context file can be found <a href="http://europepmc.org/docs/europepmc-annotation-api-vocab.json" target="_blank">here</a>. </p> <p> According to the type of annotations there are different types of JSON-LD representations:</p> <ul> <li>Named entities annotations (i.e. provided by Europe PMC) <pre class="code_rdf"> { "@context": "http://europepmc.org/docs/europepmc-annotation-api-vocab.json", # context file "id": "http://europepmc.org/article/MED/21494379#europepmc_1-1", # annotation link back "type": "Annotation", "creator": "europepmc", # provider "body": "http://purl.obolibrary.org/obo/CHEBI_29228", # uri of the tagged database entity "target": { "id": "http://europepmc.org/article/MED/21494379#europepmc_1-1", # annotation link back "source": "http://europepmc.org/article/MED/21494379", # article page url "isPartOf": "Title", # section of the article where the annotation appears "selector": { "type": "TextQuoteSelector", "exact": "Fluoride", # text of the annotation inside the article "prefix": "", # prefix of the annotation inside the article "suffix": " concentration of some brands of ferment" # suffix of the annotation inside the article } } } </pre> </li> <li> Sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) <pre class="code_rdf"> { "@context": "http://europepmc.org/docs/europepmc-annotation-api-vocab.json", # context file "id": "http://europepmc.org/abstract/MED/15892892#geneRif_356408_P36159", # annotation link back "type": "Annotation", "creator": "HES-SO / SIB Text Mining for Elixir", # provider "target": "http://purl.uniprot.org/uniprot/P36159", # uri of the tagged database entity "body": { "id": "http://europepmc.org/abstract/MED/15892892#geneRif_356408_P36159", # annotation link back "type": "TextualBody", "value": "In this work, we show that the yeast homolog of ELAC2, encoded by TRZ1 (tRNase Z 1), is involved genetically in RNA processing.", # text of the annotation inside the article "source": "http://europepmc.org/article/MED/15892892", # article page url "isPartOf": "Abstract" # section of the article where the annotation appears } } </pre> </li> <li> Annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) <pre class="code_rdf"> { "@context": "http://europepmc.org/docs/europepmc-annotation-api-vocab.json", # context file "id": "http://europepmc.org/articles/PMC3691765#openTargets_1563_Q14790_EFO_0001668", # annotation link back "type": "Annotation", "creator": "OpenTargets", # provider "target": { "type": "List", "items": [ { "id": "http://purl.uniprot.org/uniprot/Q14790", "label": "caspase 8" }, { "id": "http://www.ebi.ac.uk/efo/EFO_0001668", "label": "HPV" } ] # uri of the tagged database entities }, "body": { "id": "http://europepmc.org/articles/PMC3691765#openTargets_1563_Q14790_EFO_0001668", # annotation link back "type": "TextualBody", "value": "caspase 8 (HPV" ,# text of the annotation inside the article "source": "http://europepmc.org/articles/PMC3691765", # article page url "isPartOf": "Table" # section of the article where the annotation appears } } </pre> </li> </ul> </div> </div> <script type="text/javascript"> /*<![CDATA[*/ jQuery(function () { jQuery('body').addClass('swagger-section'); hljs.configure({ highlightSizeThreshold: 5000 }); // Pre load translate... if(window.SwaggerTranslator) { window.SwaggerTranslator.translate(); } window.swaggerUi = new SwaggerUi({ url: "https://www.ebi.ac.uk/europepmc/annotations_api/v2/api-docs.json", //url: "http://dev.europepmc.org/europepmc/annotations_api/v2/api-docs.json", dom_id: "swagger-ui-container", supportedSubmitMethods: ['get'], docExpansion: "list", jsonEditor: false, defaultModelRendering: 'example', showRequestHeaders: false, showOperationIds: false, validatorUrl:null, onComplete: function() { $('#api_info').after('<p>We advise that you read our Privacy Notice before using this API. 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