Colil: a database and search service for citation contexts in the life sciences domain

Fujiwara, Toyofumi; Yamamoto, Yasunori

doi:10.1186/s13326-015-0037-x

“…While semantic annotations make it possible to define very specific queries, federated SPARQL makes it possible merge data distributed across the web. The researcher may also be interested in complementing the results with information from the Colil database ( Fujiwara & Yamamoto, 2015 ). Colil searches for a cited paper in the Colil database and then returns a list of the citation contexts and relevant papers based on co-citations.…”

Section: Resultsmentioning

confidence: 99%

Biotea: semantics for Pubmed Central

García

¹

,

López

²

,

García

³

et al. 2018

PeerJ

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A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io.

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“…This is why most of the literature concerning extended CC rather provides adaptive methods. A mention is needed to the work of Fujiwara and Yamamoto (2015), mostly for their overall project than for the CC retrieval approach which relies on a very basic technique (they include the sentence after the citing one if the reference marker is at the end of the citing sentence and limit long citing sentences to 240 characters before and after citation markers). The authors built the Colil database where CC of the life sciences domain are stored, and made it available to users through a web-based search service.…”

Section: Fixed Extended Contextmentioning

confidence: 99%

Identifying Citation Contexts: a Review of Strategies and Goals.

Rotondi¹,

Iorio²,

Limpens³

2018

Proceedings of the Fifth Italian Conference on Computational Linguistics CLiC-it 2018

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English. The Citation Contexts of a cited entity can be seen as little tesserae that, fit together, can be exploited to follow the opinion of the scientific community towards that entity as well as to summarize its most important contents. This mosaic is an excellent resource of information also for identifying topic specific synonyms, indexing terms and citers' motivations, i.e. the reasons why authors cite other works. Is a paper cited for comparison, as a source of data or just for additional info? What is the polarity of a citation? Different reasons for citing reveal also different weights of the citations and different impacts of the cited authors that go beyond the mere citation count metrics. Identifying the appropriate Citation Context is the first step toward a multitude of possible analysis and researches. So far, Citation Context have been defined in several ways in literature, related to different purposes, domains and applications. In this paper we present different dimensions of Citation Context investigated by researchers through the years in order to provide an introductory review of the topic to anyone approaching this subject. Italiano. Possiamo pensare ai Contesti Citazionali come tante tessere che, unite, possono essere sfruttate per seguire l'opinione della comunità scientifica riguardo ad un determinato lavoro o per riassumerne i contenuti più importanti. Questo mosaico di informazioni può essere utilizzato per identificare sinonimi specifici e Index Terms nonchè per individuare i motivi degli autori dietro le citazioni. Identificare il Contesto Citazionale ottimaleè il primo passo per numerose analisi e ricerche. Il Contesto Citazionaleè stato definito in diversi modi in letteratura, in relazione a differenti scopi, domini e applicazioni. In questo paper presentiamo le principali dimensioni testuali di Contesto Citazionale investigate dai ricercatori nel corso degli anni.

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“…While semantic annotations make it possible to define very specific queries, federated SPARQL makes it possible merge data distributed across the web. The researcher may also be interested in complementing the results with information from the Colil database (Fujiwara and Yamamoto, 2015). Colil searches for a cited paper in the Colil database and then returns a list of the citation contexts and relevant papers based on co-citations.…”

Section: In and Out The Content Making Use Of Linked Datamentioning

confidence: 99%

Biotea, semantics for Pubmed Central

García

¹

,

Gómez

²

,

García

³

et al. 2017

Preprint

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A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Availability A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases.

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Colil: a database and search service for citation contexts in the life sciences domain

Cited by 22 publications

References 11 publications

Biotea: semantics for Pubmed Central

Biotea: semantics for Pubmed Central

Identifying Citation Contexts: a Review of Strategies and Goals.

Biotea, semantics for Pubmed Central

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