Core Technology Development Team Meeting

Transcription

1 Core Technology Development Team Meeting

2 Agenda v Updates regarding last meeting action items v Presentation by Ergin about Ontology Services v Brief updates from others Supported by the NIH grant 1U24 AI to the University of California, San Diego 2

3 Updates Action Items v PP 3.2 Updated Progress report sent to all team members. Decide whether it should be integrated into prototype. v RFA for PP 4.1 update : EC has until 07/28 to comment on the RFA Supported by the NIH grant 1U24 AI to the University of California, San Diego 3

4 Updates Action Items v Spreadsheet defining component/type of Pilot Project integration for each PP Title Linking publica-ons and underlyinglinking publica-ons and underlying datasets using natural language processing Data Recommenda-on Using Machine Learning and Crowdsourcing Intelligent Search Expansion and Visualiza-on of Datasets (isee- DELVE) Development of Cita-on and Data Access Metrics applied to RCSB Protein Data Bank and related Resources Component/mode of integra5on 1) Type specific advanced search op-on in the prototype. 2) Poten-al methodology to extract metadata about datasets from associated literature 1) Bipar-te graph (datasets and PMID) could be used to incorporate the number of cita-ons to a dataset into the ranking func-on of the prototype 2) Given the cita-on index of ar-cle, do something similar to PageRank wherein the cita-ons to the ci-ng ar-cles are also considered 1) Build in algorithm into search engine for query expansion (isee). 2) DELVE could be presented as a separate interface with innova-ve and exploratory search and visualiza-on op-ons for the user Maybe integrated? Supported by the NIH grant 1U24 AI to the University of California, San Diego 4

5 Discussion v Unify on UMLS vs. specialize on each terminology? v Relationships other than parent-child w Is_a, part_of w Synonyms (exact, broad, narrow) v Infer sibling information? v Obsolete concepts/relationships v To Go: UBERON, Disease Ontology,? w Protein

6 Tasks Task Select platform Select terminology/onto. Generate unified ontology Validate ontology Implement services P P P * P ** (*) UBERON, Disease Ontology (**) GO and HGNC

7 Platform v Graph Db (SciGraph, neo4j) v Elasticsearch w String à Concept

8 Tasks Task Select platform Select terminology/onto. Generate unified ontology Validate ontology Implement services P P P * P ** (*) UBERON, Disease Ontology (**) GO and HGNC

9 TermServ Content v MeSH v SNOMED CT v NBCI v FMA v GO 1 Problem Chemical Gene-Protein 2 Procedure Body Loc/Sys Organism v HGNC v UBERON, Disease Ontology

10 MeSH MSH CHD NULL MSH PAR NULL MSH QB NULL MSH RB inverse_isa MSH RB mapped_from MSH RB NULL MSH RN isa MSH RN mapped_to MSH RN NULL MSH RO has_mapping_qualifier MSH RO mapping_qualifier_of MSH RO NULL MSH SIB NULL MSH SY entry_version_of MSH SY expanded_form_of 83 MSH SY has_entry_version MSH SY has_expanded_form 83 MSH SY has_permuted_term MSH SY has_sort_version 3930 MSH SY permuted_term_of MSH SY sort_version_of 3930

11 NCBI Taxonomy NCBI CHD NULL NCBI PAR NULL NCBI SY expanded_form_of 217 NCBI SY has_expanded_form 217

12 SNOMED CT 179 relationship types SNOMEDCT_US CHD isa SNOMEDCT_US PAR inverse_isa SNOMEDCT_US RB alternative_of 181 SNOMEDCT_US RB has_part SNOMEDCT_US RB inverse_was_a SNOMEDCT_US RB mapped_from SNOMEDCT_US RB mapped_to 886 SNOMEDCT_US RB referred_to_by 872 SNOMEDCT_US RN has_alternative 181 SNOMEDCT_US RN mapped_from 886 SNOMEDCT_US RN mapped_to SNOMEDCT_US RN part_of SNOMEDCT_US RN refers_to 872 SNOMEDCT_US RN was_a SNOMEDCT_US RO access_device_used_by 2906 SNOMEDCT_US RO access_instrument_of 3410

13 FMA 93 relationship types FMA CHD isa FMA PAR inverse_isa FMA RO adheres_to 7 FMA RO adjacent_to 22 FMA RO afferent_to 794 FMA RO arterial_supply_of 628 FMA RO articulates_with 672 FMA RO attaches_to 197 FMA RO attributed_constitutional_part_of 30 FMA RO attributed_continuous_with 1540 FMA RO attributed_part_of 1635 FMA RO attributed_regional_part_of 17 FMA RO bounded_by 447 FMA RO bounds 447 FMA RO branch_of 7188 FMA RO cell_connecting_part_of 4 FMA RO cell_shape_of 1 FMA RO cell_surface_specialization_of 2 FMA RO constitutional_part_of FMA RO contained_in 690 FMA RO contains 690 FMA RO continuation_branch_of 2

14 Gene Ontology GO CHD isa GO PAR inverse_isa GO RB has_part 9859 GO RB inverse_isa 9295 GO RB NULL GO RN isa 9295 GO RN NULL GO RN part_of 9859 GO RO has_occurrence 159 GO RO negatively_regulated_by 4800 GO RO negatively_regulates 4800 GO RO NULL GO RO occurs_in 159 GO RO positively_regulated_by 4748 GO RO positively_regulates 4748 GO RO regulated_by 5598 GO RO regulates 5598 GO RQ consider 1551 GO RQ consider_from 1551 GO RQ replaced_by 732 GO RQ replaces 732 GO SIB NULL GO SY mth_expanded_form_of 3258 GO SY mth_has_expanded_form 3258 GO SY NULL

15 HGNC HGNC SY alias_of HGNC SY expanded_form_of HGNC SY has_alias HGNC SY has_expanded_form 38707

16 To Do v UBERON v Disease ontology

17 Discussion v Unify on UMLS vs. specialize on each terminology? v Relationships other than parent-child w Is_a, part_of w Synonyms (exact, broad, narrow) v Infer sibling information? v Obsolete concepts/relationships v To Go: UBERON, Disease Ontology,? w Protein

18 Other issues v other issues? v Thank You