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<p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><b><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black">Task:</span></b><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black"> We call for automated systems to
extract and normalize the findings of dysmorphology physical examinations. The
dataset consists of 3136 de-identified observations with dysmorphic
findings manually annotated and normalized with their corresponding </span><a href="https://hpo.jax.org/app/" title="Original URL:
https://urldefense.com/v3/__https:/hpo.jax.org/app/__;!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMczH2Z9A$
Click to follow link."><span style="font-size:9pt;font-family:"Times New Roman",serif;color:rgb(0,0,98)">HumanPhenotype Ontology</span></a><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black"> (HPO) terms.</span></p><p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black"><br></span></p><p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><b><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black">Motivation:</span></b><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black"> Dysmorphology physical
examinations catalog minor morphological differences of patients’ bodies and
may also identify general medical signs such as neurologic dysfunction. These findings
enable correlations of patients with known rare genetic diseases and allow
researchers to delineate undescribed genetic conditions. These medical findings
are nearly always captured as unstructured free text within the electronic
health record, making them unavailable for downstream computational analysis.
Advanced natural language processing methods are therefore required to retrieve
the information from the records.<span></span></span></p>
<p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black"> <span></span><span> <br></span></span></p>
<p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><b><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black">Challenge:</span></b><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black"> Both extraction and
normalization are challenging. The extraction is challenging due to the
descriptive style of the examinations which, for conciseness, report findings
with disjoint and overlapping mentions. The normalization is challenging due to
the large scale of the HPO ontology which requires a normalizer to learn the
task without supervision since our training set does not provide examples of
all terms in the HPO. <span></span> <span></span></span></p>
<p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black">See </span><a href="https://biocreative.bioinformatics.udel.edu/tasks/biocreative-viii/track-3/" title="Original URL:
https://biocreative.bioinformatics.udel.edu/tasks/biocreative-viii/track-3/
Click to follow link."><span style="font-size:9pt;font-family:"Times New Roman",serif;color:rgb(4,74,145)">https://biocreative.bioinformatics.udel.edu/tasks/biocreative-viii/track-3/</span></a><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black"> for
details., in short: <span></span></span></p>
<ul style="margin-top:0in;margin-bottom:0in" type="disc"><li class="MsoNormal" style="color:black;margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><span style="font-size:9pt;font-family:"Times New Roman",serif">3136
de-identified observations with dysmorphic and normal findings manually
annotated and normalized with their corresponding </span><span style="color:windowtext"><a href="https://hpo.jax.org/app/" title="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fhpo.jax.org%2Fapp%2F__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMczH2Z9A%24&data=05%7C01%7CCA"><span style="font-size:9pt;font-family:"Times New Roman",serif;color:rgb(0,0,98)">Human Phenotype Ontology</span></a></span><span style="font-size:9pt;font-family:"Times New Roman",serif"> terms<span></span></span></li></ul>
<ul style="margin-top:0in;margin-bottom:0in" type="disc"><li class="MsoNormal" style="color:rgb(0,0,98);margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black">Baseline systems available (e.g. </span><span style="color:windowtext"><a href="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fdoi.org%2F10.1093%2Fnar%2Fgkz386__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMmoBx7To%24&data=05%7C01%7CCAMPBELLIM%40chop.edu%7C29f04983ec7343b4f41708db3b8c57be%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C638169246199221115%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=hux0LlF4U0GT6HWpO%2FY8JjqYLWB6WrkSMcl7RPGlF08%3D&reserved=0" title="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fdoi.org%2F10.1093%2Fnar%2Fgkz386__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMmoBx7To%24&data="><span style="font-size:9pt;font-family:"Times New Roman",serif;color:rgb(0,0,98)">doc2HPO</span></a></span><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black">, <a href="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fdoi.org%2F10.2196%2F12596__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMNZ4HF7s%24&data=05%7C01%7CCAMPBELLIM%40chop.edu%7C29f04983ec7343b4f41708db3b8c57be%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C638169246199221115%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=B2pqq50tjZ1QJtfESjbiiequC%2BGte1b%2BrxPQ3%2BrjAd0%3D&reserved=0" title="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fdoi.org%2F10.2196%2F12596__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMNZ4HF7s%24&data=05%7C01"><span style="color:rgb(0,0,98)">NeuralCR</span></a>, <a href="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fdoi.org%2F10.1093%2Fbioinformatics%2Fbtab019__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMn6mBH0w%24&data=05%7C01%7CCAMPBELLIM%40chop.edu%7C29f04983ec7343b4f41708db3b8c57be%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C638169246199221115%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=b527AtyQQb6mRMU8KSdw7L2APgTzM5Zf6ESNax9VO%2B4%3D&reserved=0" title="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fdoi.org%2F10.1093%2Fbioinformatics%2Fbtab019__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMn6mB"><span style="color:rgb(0,0,98)">PhenoTagger</span></a>, <a href="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fdoi.org%2F10.1109%2FTCBB.2022.3170301__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMHtsRXdg%24&data=05%7C01%7CCAMPBELLIM%40chop.edu%7C29f04983ec7343b4f41708db3b8c57be%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C638169246199221115%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=V%2BJKQHfBB7Jj6LqzwzAE7bIJ0NWitzhILOpekgbMf9w%3D&reserved=0" title="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fdoi.org%2F10.1109%2FTCBB.2022.3170301__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMHtsRXdg%24&"><span style="color:rgb(0,0,98)">PhenoBERT</span></a>, and </span><span style="color:windowtext"><a href="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2FGeneDx%2Ftxt2hpo__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMeawcndc%24&data=05%7C01%7CCAMPBELLIM%40chop.edu%7C29f04983ec7343b4f41708db3b8c57be%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C638169246199221115%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mtCRgl7GcWjWcSArggA%2FbhlbAnDpwZtty0reoUuDrWI%3D&reserved=0" title="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2FGeneDx%2Ftxt2hpo__%3B!!KOmnBZxC8_2BBQ!wOul5WmKEXAz3ieVMFnkWsnE22f7qVws_GT94mj2AxE_p9hY_nBY3f4pCJT10h7WmZyFYl5nLY7QhOPrSRJMeawcndc%24&data=05%"><span style="font-size:9pt;font-family:"Times New Roman",serif;color:rgb(0,0,98)">txt2HPO</span></a></span><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black">)</span><span style="font-size:9pt;font-family:"Times New Roman",serif"><span></span></span></li></ul>
<ul style="margin-top:0in;margin-bottom:0in" type="disc"><li class="MsoNormal" style="color:black;margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><span style="font-size:9pt;font-family:"Times New Roman",serif">Codalab opened
at </span><span style="color:windowtext"><a href="https://codalab.lisn.upsaclay.fr/competitions/11351" title="Original URL:
https://codalab.lisn.upsaclay.fr/competitions/11351
Click to follow link."><span style="font-size:9pt;font-family:"Times New Roman",serif;color:rgb(4,74,145)">https://codalab.lisn.upsaclay.fr/competitions/11351</span></a></span><span style="font-size:9pt;font-family:"Times New Roman",serif"><span></span></span></li></ul>
<ul style="margin-top:0in;margin-bottom:0in" type="disc"><li class="MsoNormal" style="color:black;margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><span style="font-size:9pt;font-family:"Times New Roman",serif">Evaluation
period: Sept. 15, 9:00 UTC - Sept. 18, 23:59 UTC<span></span></span></li></ul>
<p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black"> <span></span></span></p>
<p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black">[Apologies for cross-posting]<span></span></span></p>
<p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:"Calibri",sans-serif"><span style="font-size:9pt;font-family:"Times New Roman",serif;color:black">Best regards,<span></span></span></p>
<span style="font-size:9pt;font-family:"Times New Roman",serif;color:black">Davy</span>
</div>