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class="Ce1Y1c" style="top: -12px"><svg class="vu8Pwe tCHXDc YSH9J" viewBox="0 0 24 24" focusable="false"><path d="M15.5 14h-.79l-.28-.27C15.41 12.59 16 11.11 16 9.5 16 5.91 13.09 3 9.5 3S3 5.91 3 9.5 5.91 16 9.5 16c1.61 0 3.09-.59 4.23-1.57l.27.28v.79l5 4.99L20.49 19l-4.99-5zm-6 0C7.01 14 5 11.99 5 9.5S7.01 5 9.5 5 14 7.01 14 9.5 11.99 14 9.5 14z"/><path d="M0 0h24v24H0z" fill="none"/></svg></span></span></div></div></div><div jsname="mADGA" class="zDUgLc"></div></div><div class="TxnWlb" jsname="BDdyze" jsaction="click:LUvzV"></div></div></header><div role="main" tabindex="-1" class="UtePc RCETm" dir="ltr"><section id="h.p_ID_3" class="yaqOZd LB7kq gk8rDe" style=""><div class="IFuOkc"></div><div class="mYVXT"><div class="LS81yb VICjCf j5pSsc db35Fc" tabindex="-1"><div class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd purZT-AhqUyc-II5mzb ZcASvf-AhqUyc-II5mzb pSzOP-AhqUyc-qWD73c Ktthjf-AhqUyc-qWD73c JNdkSc SQVYQc"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"><div class="oKdM2c ZZyype Kzv0Me"><div id="h.p_ID_5" class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd jXK9ad D2fZ2 zu5uec OjCsFc dmUFtb wHaque g5GTcb JYTMs"><div class="jXK9ad-SmKAyb"><div class="tyJCtd mGzaTb Depvyb baZpAe lkHyyc"><h2 id="h.p_ID_13" class="CDt4Ke zfr3Q JYVBee" style="text-align: left;">PheneBank</h2></div></div></div></div></div></div></div></div></div></section><section id="h.p_ID_18" class="yaqOZd" style=""><div class="IFuOkc"></div><div class="mYVXT"><div class="LS81yb VICjCf j5pSsc db35Fc" tabindex="-1"><div class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd purZT-AhqUyc-II5mzb ZcASvf-AhqUyc-II5mzb pSzOP-AhqUyc-qWD73c Ktthjf-AhqUyc-qWD73c JNdkSc SQVYQc"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"><div class="oKdM2c ZZyype Kzv0Me"><div id="h.p_ID_24" class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd jXK9ad D2fZ2 zu5uec OjCsFc dmUFtb wHaque g5GTcb JYTMs"><div class="jXK9ad-SmKAyb"><div class="tyJCtd mGzaTb Depvyb baZpAe"><p id="h.p_ID_32" class="CDt4Ke zfr3Q">About</p><p id="h.p_ID_34" class="CDt4Ke zfr3Q">Free text scientific literature has the potential to be an incredibly valuable source of data for uncovering the often hidden relationships between genes, diseases and phenotypes. Phenotypic descriptions cover abnormalities in anatomical structures, processes and behaviours. For example 'growth delay' and 'body weight loss'. Such descriptions form the basis for determining the existence and treatment of a disease but, because of their inherent complexity, have previously received less attention by the text mining community. In recent years, significant effort has been spent by a small number of expert curators to create coding systems for phenotypes (called "ontologies"), such as the Human Phenotype Ontology (HP) and the Mammalian Phenotype Ontology (MP). The PheneBank project proposes to support and speed up curation using terms discovered directly from the literature and to automatically integrate them with such standard ontologies.</p><p id="h.p_ID_36" class="CDt4Ke zfr3Q">The project seeks to harness texts for extracting statistically significant associations between phenotypes, diseases and genes. Earlier approaches have suffered from not providing deep semantic descriptions of the relations they tried to target. This means that association scores merge notions of genetic, pharmacological, and epidemiological relations etc. without distinction. Our parsing-based approach is an attempt to overcome this issue by discovering more precise relationships. The approach builds on ground breaking research at the European Bininformatics Institute by the PI (Collier) and the Wellcome Trust Sanger Instittue by the Co-investigator (Smedley), including terminology alignment of phenotypes using pairwise scoring of the conceptual elements that make up the phenotype.</p><p id="h.p_ID_38" class="CDt4Ke zfr3Q">Publications</p><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_40" class="TYR86d Sn3DJc zfr3Q">Verspoor, K., Oellrich, A., Collier, N., Groza, T., Rocca-Serra, P., Soldatova, L., ... & Shah, N. (2016), "Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop", Journal of Biomedical Semantics, 7(1), 60. [<a class="dhtgD aw5Odc" href="https://www.google.com/url?q=https%3A%2F%2Fjbiomedsem.biomedcentral.com%2Farticles%2F10.1186%2Fs13326-016-0108-7&sa=D&sntz=1&usg=AOvVaw3XIeTraAr47HvgaH7N2Abx" target="_blank">html</a>]</li><li id="h.p_ID_42" class="TYR86d Sn3DJc zfr3Q">Le, H.Q., Tran, M.V., Dang, T.H. Ha, Q.T. and Collier, N. (2016), “Sieve-based coreference resolution enhances semi-supervised learning model for chemical-induced disease relation extraction”, in Database, Oxford University Press, vol. 2016: article ID baw102; DOI: 10.1093/database/baw102. [<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4962668%2Fpdf%2Fbaw102.pdf&sa=D&sntz=1&usg=AOvVaw26zd1zAF7t3cE28YV8sl6B" target="_blank">pdf</a>]</li><li id="h.p_ID_44" class="TYR86d Sn3DJc zfr3Q">Pilehvar, M. T., Camacho-Collados, J., Navigli, R. and Collier, N. (2017), "Towards a Seamless Integration of Word Senses into Downstream NLP Applications", in Proceedings of the Association of Computational Linguistics Annual Meeting (ACL 2017), Vancouver, Canada, August (in press).</li><li id="h.p_ID_46" class="TYR86d Sn3DJc zfr3Q">Pilehvar, M. T. and Collier, N. (2017), "Inducing Representations for Rare Words by Leveraging Lexical Resources", in Proceedings of the European Chapter of the Association for Computational Linguistics (EACL), Valencia, Spain (in press) [<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.pilevar.com%2Ftaher%2Fpubs%2FPilehvar_Collier_EACL2017.pdf&sa=D&sntz=1&usg=AOvVaw05F08VV_Z2Ta3kcyzjKnxt" target="_blank">pdf</a>].</li><li id="h.p_ID_48" class="TYR86d Sn3DJc zfr3Q">Pilehvar, M. T. and Collier, N. (2016), “De-conflating semantic representations of words by exploiting knowledge from semantic networks”, in Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP 2016), Austin, USA, November 1<sup>st</sup> to 5<sup>th</sup> [<a class="dhtgD aw5Odc" href="https://www.google.com/url?q=https%3A%2F%2Farxiv.org%2Fpdf%2F1608.01961.pdf&sa=D&sntz=1&usg=AOvVaw3yQ1vpzcyUh07NsguRB1s2" target="_blank">pdf</a>].</li><li id="h.p_ID_50" class="TYR86d Sn3DJc zfr3Q">Pilehvar, M. T. and Collier, N. (2016), “Improved Semantic Representation for Domain-Specific Entities”, in Proc. BioNLP 2016 at the 2016 Annual Meeting of the Association for Computational Linguistics (ACL 2016), Berlin, Germany, August 12<sup>th</sup> to 13<sup>th </sup>[<a class="dhtgD aw5Odc" href="https://www.google.com/url?q=https%3A%2F%2Faclweb.org%2Fanthology%2FW%2FW16%2FW16-2902.pdf&sa=D&sntz=1&usg=AOvVaw3IVqSZFD27FC_VQYpkPprt" target="_blank">pdf</a>] [<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.pilevar.com%2Ftaher%2Fpubs%2FPilehvar_Collier_2016a_slides.pdf&sa=D&sntz=1&usg=AOvVaw0EJIO72dUnKjsBUJ_9L8V8" target="_blank">slides</a>].</li></ul><p id="h.p_ID_52" class="CDt4Ke zfr3Q">Data Sets</p><p id="h.p_ID_54" class="CDt4Ke zfr3Q">Outreach</p><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_56" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc">List of text mining tools</a></li><li id="h.p_ID_58" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fhealtex.org%2Fevent%2Fhealtex-launch%2F&sa=D&sntz=1&usg=AOvVaw241YWeAMugGCH_vUz2azAv" target="_blank">Invited talk</a> given at the EPSRC HealTex Network Launch Event (November 2016)</li><li id="h.p_ID_60" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc" href="https://www.google.com/url?q=https%3A%2F%2Fjbiomedsem.biomedcentral.com%2Farticles%2F10.1186%2Fs13326-016-0108-7&sa=D&sntz=1&usg=AOvVaw3XIeTraAr47HvgaH7N2Abx" target="_blank">PhenoDay 2016</a> was a joint workshop held with Bio-Ontologies at ISMB (July 2016)</li><li id="h.p_ID_62" class="TYR86d Sn3DJc zfr3Q">Seminar at the European Bioinformatics Institute, Cambridge (September 2015)</li><li id="h.p_ID_64" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc" href="https://www.google.com/url?q=https%3A%2F%2Fwww.bigdata.cam.ac.uk%2Fevents%2Fevents-archive%2F2015-events%2Fbig-data-in-medicine-exemplars-and-opportunities-in-data-science%2Fundiscovered-scientific-knowledge-from-large-unstructured-text-collections-in-an-era-of-big-data&sa=D&sntz=1&usg=AOvVaw1Mxvv_dGgGo0pvvcB9h7Th" target="_blank">Invited talk</a> given at the Big Data in Medicine Workshop, Cancer Research UK Cambridge Institute (June 2015)</li></ul><p id="h.p_ID_66" class="CDt4Ke zfr3Q">Collaborators</p><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_68" class="TYR86d Sn3DJc zfr3Q">Damian Smedley (Queen Mary University London)</li><li id="h.p_ID_70" class="TYR86d Sn3DJc zfr3Q">Anna Korhonen (University of Cambridge)</li><li id="h.p_ID_72" class="TYR86d Sn3DJc zfr3Q">Bill Skarnes (Wellcome Trust Sanger Institute)</li><li id="h.p_ID_74" class="TYR86d Sn3DJc zfr3Q">Dietrich Rebholz-Schuhmann (INSIGHT, National University of Ireland at Galway)</li><li id="h.p_ID_76" class="TYR86d Sn3DJc zfr3Q">Peter Robinson (The Jackson Laboratory)</li><li id="h.p_ID_78" class="TYR86d Sn3DJc zfr3Q">Hoang Quynh Le (University of Vietnam)</li><li id="h.p_ID_80" class="TYR86d Sn3DJc zfr3Q">Jo McEntyre (EMBL-EBI)</li><li id="h.p_ID_82" class="TYR86d Sn3DJc zfr3Q">Paul Lasco (McGill University)</li><li id="h.p_ID_84" class="TYR86d Sn3DJc zfr3Q">Lawrence Hunter (University of Colorado at Denver)</li><li id="h.p_ID_86" class="TYR86d Sn3DJc zfr3Q">Robert Stevens (University of Manchester)</li></ul><p id="h.p_ID_88" class="CDt4Ke zfr3Q">Funding</p><p id="h.p_ID_90" class="CDt4Ke zfr3Q">PheneBank is funded by an Medical Research Council grant (MR/M025160/1).</p></div></div></div></div></div></div></div></div></div></section></div><div class="Xpil1b xgQ6eb"></div><footer jsname="yePe5c"></footer><div jscontroller="j1RDQb" jsaction="rcuQ6b:rcuQ6b;MxH79b:JdcaS;FaOgy:XuHpsb;" class="dZA9kd ynRLnc" data-last-updated-at-time="1594658374611" data-is-preview="false"><div role="button" class="U26fgb JRtysb WzwrXb I12f0b K2mXPb zXBiaf ynRLnc" jscontroller="iSvg6e" jsaction="click:cOuCgd; 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