A few contributions of the SIFR project

Transcription

1 A few contributions of the SIFR project Semantic Indexing of French biomedical Resources Data seminar- December 10th 2015 LIRMM University of Montpellier Clement Jonquet, Mathieu Roche, Sandra Bringay et al.

2 Biologists have adopted ontologies To provide canonical representation of scientific knowledge To annotate experimental data to enable interpretation, comparison, and discovery across databases To facilitate knowledge-based applications for Decision support Natural language-processing Data integration But ontologies are: spread out, in different formats, of different size, with different structures UMLS (163 databases) : ~ terms in English / ~ tems in Spanish ~ terms in French

3 Comparison of the approaches [IWBBIO'14]

4 Annotation challenge Explosion of biomedical data: diverse, distributed, unstructured not link to ontologies RESOURCES Hard for biomedical researchers to find the data they need Data integration problem Translational discoveries are prevented Good examples GO annotations PubMed (biomedical literature) indexed with Mesh headings ONTOLOGIES

5 Semantic Indexing of French Biomedical Data Resources project in collaboration with

6 Use biomedical ontologies-based annotations end-user applications Researchers A Annotation produce Ontologies MeSH 2015 SNOMED DATA B Enrichment

7 SIFR axes of research (1/8): Design of the SIFR (French) Annotator service Deployment of a local instance of BioPortal at LIRMM 16 French terminologies imported from UMLS, EHTOP & BioPortal New improvement to the annotation workflow Automatic term extraction measures (C-value, LIDF-value, etc.) Scoring of annotations & representation in RDF using the AO [SWAT4LS 2014]

8 SIFR axes of research (2/8): Dealing with multilingualism within BioPortal Status of multilingualism in BioPortal quite negative Set of propositions [MSW 2014] Representation of natural language property for an ontology Representation of the distinction between ontologies Representation of relation between ontologies Representation of multilingual translation mappings Reconciliation of multilingual mappings Currently being tested/implemented within our local instance

9 SIFR axes of research (3/8): Automatic extraction of biomedical terminology from text Context of the PhD of Juan Antonio Lossio [TALN 2014][PolTAL 2014][IRJ 2015] BioTex, software [ISWC 2014] Work in French, English, and Spanish Motivations for automatic terminology extraction Experiment and validate approaches for French data Contribute to the ontology enrichment process Acquire some NLP expertise for the annotation workflow

10 SIFR axes of research (4/8): Semantic distance framework Automatically compute existing (Rada, Wu&Palmer, Resnik) semantic similarity measures over BioPortal ontologies For a given concept get all semantically closed concepts Get the semantic distance between 2 concepts Collaboration with LGI2P to reuse Semantic Measure Library (SML) within BioPortal 1 st prototype: To include SML within BioPortal backend to bring semantic distance services to the ontologies and data annotated

11 SIFR axes of research (5/8): Informal patient data analysis Dealing with public patient data on blogs, forums and tweets Detection of emotion [EGC 2014][eTELEMED 2014] Patient vocabulary (crabe vs. cancer) Project Parlons de nous ( MSH-M A vocabulary currently being constructed Hosted and available in our local instance of BioPortal Used for annotations, indexing

12 SIFR axes of research (6/8): Semantic indexing of semantic Web data and social Web data - Viewpoint project Graph based knowledge representation formalism Collaboration with P. Lemoisson (CIRAD) PhD project of Guillaume Surroca First prototype for semantic search over HAL-LIRMM publications [IC2014] Toward a model for Serendipity and collective intelligence [KEOD2015]

13 SIFR axes of research (7/8): pharmacogenomics use case PGx studies how individual gene variations cause variability in drug responses Validation of pharmacogenomics state-of-the-art knowledge on the basis of practice-based evidences Compare pharmacogenomics literature (in English) and electronic health records (in French) EHRs from Paris (HEGP) & St Etienne hospitals Improvement of the Annotator in order to handle clinical data: negation, disambiguation, modularity, temporality ANR Collaborative action lead by Adrien Coulet (LORIA) Stanford is in the loop (Russ, Mark, Michel, Nigam)

14 SIFR axes of research (8/8): AgroPortal project In collaboration with the Institute of Computational Biology of Montpellier Design of a semantic annotation workflow for plant data - collaboration with IBC project [CO-PDI 2014] AgroLD: to build an RDF knowledge base to house plant data resources: SouthGreen, Gramene, OryGeneDB [RDA 2014] In collaboration with CIRAD/IRD, INRA, and Bioversity International Experiment NCBO technologies for the plant community Help the design and evolution of Cropontology.org 1-year postdoc starting in June Interactions with NSF Planteome project (P. Jaiswal, L. Cooper)

15 Terminology extraction in Biomedecine (step 3)

16 1 Linguistic Statistic (Ranking) Graph Web (Re-ranking) 2 term1 term2 termn

17 LIDF-value Linguistic Statistic (Ranking) Graph Web term1 term2 termn

18 Linguistic TF-IDF and Okapi BM25 Statistic (Ranking) Keyword Keyword Keyword Graph Web term1 term2 termn Keyword1 Keyword2

19 Web-based: WAHI buschke Linguistic «buschke lowenstein tumor» buschke lowenstein tumor lowenstein tumor Statistic WEB Graph Web (Re-ranking) term1 term2 termn nb = number of hits!

20 Experiments (quantitive evaluation) K = 100, 500,, 20000

21 Experiments (qualitative evaluation) Ontologos, VARAPP 500 candidate terms extracted from their documents Objective: extraction of relevant biomedical terms (i.e. those which can be added to a biomedical terminology) Precision True Biomedical Terms 74.6 % False Biomedical Terms 25.4 % bêta-2 mimétiques bêta-2 agonistes dosage des ige spécifiques suivi des maladies allergiques

22 A few conclusions

23 Future work Continue to move different prototypes into production Release of the French Annotator Find more use cases Collaboration with the plant/agro community Continue reusing and contributing to NCBO technology

24 Online resources Web page: To be turned into a real small web site Task & team: Feature removed by RG in February (to be replaced) Code repository: 13 developpers 10 repositories Publications: Direct link to HAL-LIRMM platform with advance search features