Literature DB >> 33479214

An empirical meta-analysis of the life sciences linked open data on the web.

Maulik R Kamdar1,2, Mark A Musen3.   

Abstract

While the biomedical community has published several "open data" sources in the last decade, most researchers still endure severe logistical and technical challenges to discover, query, and integrate heterogeneous data and knowledge from multiple sources. To tackle these challenges, the community has experimented with Semantic Web and linked data technologies to create the Life Sciences Linked Open Data (LSLOD) cloud. In this paper, we extract schemas from more than 80 biomedical linked open data sources into an LSLOD schema graph and conduct an empirical meta-analysis to evaluate the extent of semantic heterogeneity across the LSLOD cloud. We observe that several LSLOD sources exist as stand-alone data sources that are not inter-linked with other sources, use unpublished schemas with minimal reuse or mappings, and have elements that are not useful for data integration from a biomedical perspective. We envision that the LSLOD schema graph and the findings from this research will aid researchers who wish to query and integrate data and knowledge from multiple biomedical sources simultaneously on the Web.

Entities:  

Year:  2021        PMID: 33479214      PMCID: PMC7819992          DOI: 10.1038/s41597-021-00797-y

Source DB:  PubMed          Journal:  Sci Data        ISSN: 2052-4463            Impact factor:   6.444


  52 in total

1.  SNOMED clinical terms: overview of the development process and project status.

Authors:  M Q Stearns; C Price; K A Spackman; A Y Wang
Journal:  Proc AMIA Symp       Date:  2001

2.  Text Snippets to Corroborate Medical Relations: An Unsupervised Approach using a Knowledge Graph and Embeddings.

Authors:  Maulik R Kamdar; Craig E Stanley; Michael Carroll; Linda Wogulis; William Dowling; Helena F Deus; Mevan Samarasinghe
Journal:  AMIA Jt Summits Transl Sci Proc       Date:  2020-05-30

3.  The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository.

Authors:  Kenneth Clark; Bruce Vendt; Kirk Smith; John Freymann; Justin Kirby; Paul Koppel; Stephen Moore; Stanley Phillips; David Maffitt; Michael Pringle; Lawrence Tarbox; Fred Prior
Journal:  J Digit Imaging       Date:  2013-12       Impact factor: 4.056

4.  The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

Authors:  Janna Hastings; Leonid Chepelev; Egon Willighagen; Nico Adams; Christoph Steinbeck; Michel Dumontier
Journal:  PLoS One       Date:  2011-10-03       Impact factor: 3.240

5.  The IntAct molecular interaction database in 2012.

Authors:  Samuel Kerrien; Bruno Aranda; Lionel Breuza; Alan Bridge; Fiona Broackes-Carter; Carol Chen; Margaret Duesbury; Marine Dumousseau; Marc Feuermann; Ursula Hinz; Christine Jandrasits; Rafael C Jimenez; Jyoti Khadake; Usha Mahadevan; Patrick Masson; Ivo Pedruzzi; Eric Pfeiffenberger; Pablo Porras; Arathi Raghunath; Bernd Roechert; Sandra Orchard; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2011-11-24       Impact factor: 16.971

6.  The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

Authors:  Mark D Wilkinson; Benjamin Vandervalk; Luke McCarthy
Journal:  J Biomed Semantics       Date:  2011-10-24

7.  neXtProt: a knowledge platform for human proteins.

Authors:  Lydie Lane; Ghislaine Argoud-Puy; Aurore Britan; Isabelle Cusin; Paula D Duek; Olivier Evalet; Alain Gateau; Pascale Gaudet; Anne Gleizes; Alexandre Masselot; Catherine Zwahlen; Amos Bairoch
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

8.  BioGRID: a general repository for interaction datasets.

Authors:  Chris Stark; Bobby-Joe Breitkreutz; Teresa Reguly; Lorrie Boucher; Ashton Breitkreutz; Mike Tyers
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

9.  Ensembl 2016.

Authors:  Andrew Yates; Wasiu Akanni; M Ridwan Amode; Daniel Barrell; Konstantinos Billis; Denise Carvalho-Silva; Carla Cummins; Peter Clapham; Stephen Fitzgerald; Laurent Gil; Carlos García Girón; Leo Gordon; Thibaut Hourlier; Sarah E Hunt; Sophie H Janacek; Nathan Johnson; Thomas Juettemann; Stephen Keenan; Ilias Lavidas; Fergal J Martin; Thomas Maurel; William McLaren; Daniel N Murphy; Rishi Nag; Michael Nuhn; Anne Parker; Mateus Patricio; Miguel Pignatelli; Matthew Rahtz; Harpreet Singh Riat; Daniel Sheppard; Kieron Taylor; Anja Thormann; Alessandro Vullo; Steven P Wilder; Amonida Zadissa; Ewan Birney; Jennifer Harrow; Matthieu Muffato; Emily Perry; Magali Ruffier; Giulietta Spudich; Stephen J Trevanion; Fiona Cunningham; Bronwen L Aken; Daniel R Zerbino; Paul Flicek
Journal:  Nucleic Acids Res       Date:  2015-12-19       Impact factor: 16.971

10.  PhLeGrA: Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data.

Authors:  Maulik R Kamdar; Mark A Musen
Journal:  Proc Int World Wide Web Conf       Date:  2017-04
View more
  1 in total

1.  A COMPASS for VESPUCCI: A FAIR Way to Explore the Grapevine Transcriptomic Landscape.

Authors:  Marco Moretto; Paolo Sonego; Stefania Pilati; José Tomás Matus; Laura Costantini; Giulia Malacarne; Kristof Engelen
Journal:  Front Plant Sci       Date:  2022-02-24       Impact factor: 5.753

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.