BIRI specifications


Unique identifier OMICS_34049
Alternative name BioInformatics Resource Inventory
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • person_outline Guillermo de la Calle

Publication for BioInformatics Resource Inventory

BIRI citations


Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature

PLoS One
PMCID: 5156472
PMID: 26730820
DOI: 10.1371/journal.pone.0146300

[…] this end are reported in the literature [–]. OReFiL [] crawls MEDLINE abstracts and BioMed Central open-access journal full papers for URLs of resources using regular expressions and heuristic rules. Bioinformatics Resource Inventory (BIRI) [] uses NLP techniques and handcrafted regular expressions expressed as transition networks for resource naming, functionality detection and resource classific […]


Ambiguity and variability of database and software names in bioinformatics

J Biomed Semantics
PMCID: 4485340
PMID: 26131352
DOI: 10.1186/s13326-015-0026-0

[…] nd software names from the literature. For example, OReFiL [] utilises the mentions of Unified Resource Locators (URLs) in text to recognise new resources to update its own internal index. Similarly, BIRI (BioInformatics Resource Inventory) uses a series of hand crafted regular expressions to automatically capture resource names, their functionality and classification from paper titles and abstrac […]

BIRI institution(s)
Department Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Madrid, Spain
BIRI funding source(s)
Supported by the Spanish Ministry of Science and Innovation (OntoMineBase project, reference TSI2006-13021-C02-01, and COMBIOMED- RETICS), the European Commission through the ACGT integrated project (FP6-2005-IST-026996), the ACTION-Grid support action (FP7-ICT-2007-2-224176) and the Comunidad de Madrid, Spain.

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