Connectionists: 2nd CFP - Normalization of genetic phenotypes in Dysmorphology Physical Examination @ BioCreative VIII - track 3

[Davy Weissenbacher]

*Task:* We call for automated systems to extract and normalize the findings
in dysmorphology physical examinations. The dataset consists of 3136
de-identified observations with dysmorphic findings manually annotated and
normalized with their corresponding Human Phenotype Ontology (HPO) terms.
Both extraction and normalization are challenging. The extraction due to
the descriptive style of the examinations which, for conciseness, report
findings with disjoint and overlapping mentions. The normalization 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. See
https://biocreative.bioinformatics.udel.edu/tasks/biocreative-viii/track-3/
for details.

*Motivation:* The dysmorphology physical examination catalogs minor
morphological differences in patients’ bodies and may identify general
medical signs such as neurologic dysfunction. Its 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 it unavailable for downstream
computational analysis. Advanced Natural Language Processing methods are
therefore required to retrieve the information from the records.

*In short:*
• 3136 de-identified observations with dysmorphic and normal findings
manually annotated and normalized with their corresponding Human Phenotype
Ontology terms
• Baseline systems available (e.g. doc2HPO, NeuralCR, PhenoTagger,
PhenoBERT, and txt2HPO)
• Codalab opened at https://codalab.lisn.upsaclay.fr/competitions/11351
• Evaluation period: Sept. 15, 9:00 UTC - Sept. 18, 23:59 UTC

[Apologies for cross-posting]

Best regards,
Davy
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