Name
Abstract | ||
|---|---|---|
The Swiss Variant Interpretation Platform for Oncology is a centralized, joint and curated database for clinical somatic variants piloted by a board of Swiss healthcare institutions and operated by the SIB Swiss Institute of Bioinformatics. To support this effort, SIB Text Mining designed a set of text analytics services. This report focuses on three of those services. First, the automatic annotations of the literature with a set of terminologies have been performed, resulting in a large annotated version of MEDLINE and PMC. Second, a generator of variant synonyms for single nucleotide variants has been developed using publicly available data resources, as well as patterns of non-standard formats, often found in the literature. Third, a literature ranking service enables to retrieve a ranked set of MEDLINE abstracts given a variant and optionally a diagnosis. The annotation of MEDLINE and PMC resulted in a total of respectively 785,181,199 and 1,156,060,212 annotations, which means an average of 26 and 425 annotations per abstract and full-text article. The generator of variant synonyms enables to retrieve up to 42 synonyms for a variant. The literature ranking service reaches a precision (P10) of 63%, which means that almost two-thirds of the top-10 returned abstracts are judged relevant. Further services will be implemented to complete this set of services, such as a service to retrieve relevant clinical trials for a patient and a literature ranking service for full-text articles. |
Year | DOI | Venue |
|---|---|---|
2020 | 10.3233/SHTI200288 | DIGITAL PERSONALIZED HEALTH AND MEDICINE |
Keywords | DocType | Volume |
Precision medicine, literature, variant, terminology, text-mining | Conference | 270 |
ISSN | Citations | PageRank |
0926-9630 | 0 | 0.34 |
References | Authors | |
0 | 9 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Déborah Caucheteur | 1 | 0 | 0.34 |
| Julien Gobeill | 2 | 302 | 30.42 |
| Anaïs Mottaz | 3 | 0 | 0.34 |
| Emilie Pasche | 4 | 99 | 15.93 |
| Pierre-André Michel | 5 | 0 | 0.34 |
| Luc Mottin | 6 | 0 | 0.34 |
| Daniel J. Stekhoven | 7 | 65 | 5.87 |
| Valérie Barbié | 8 | 0 | 0.34 |
| patrick ruch | 9 | 117 | 22.37 |