Detection of Protein Catalytic Sites in the Biomedical Literature

Verspoor, Karin; MacKinlay, Andrew; Cohn, Judith D.; Wall, Michael E.

doi:10.1142/9789814447973_0042

Cited by 7 publications

(9 citation statements)

References 15 publications

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“…We have shown that processing full-text papers is important; this is also in agreement with prior work, e.g. the analysis of protein residues in [26], as well as the general observation of differences between abstracts and full texts, with full texts argued to have more ‘content’ [33, 34]. Importantly, our results provide a novel result, quantifying the significant role that processing of additional material linked to the article with text mining plays in increasing the coverage of extracted mutations.…”

Section: Discussionsupporting

confidence: 90%

Literature mining of genetic variants for curation: quantifying the importance of supplementary material

Jimeno-Yepes

Verspoor

2014

Database

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A major focus of modern biological research is the understanding of how genomic variation relates to disease. Although there are significant ongoing efforts to capture this understanding in curated resources, much of the information remains locked in unstructured sources, in particular, the scientific literature. Thus, there have been several text mining systems developed to target extraction of mutations and other genetic variation from the literature. We have performed the first study of the use of text mining for the recovery of genetic variants curated directly from the literature. We consider two curated databases, COSMIC (Catalogue Of Somatic Mutations In Cancer) and InSiGHT (International Society for Gastro-intestinal Hereditary Tumours), that contain explicit links to the source literature for each included mutation. Our analysis shows that the recall of the mutations catalogued in the databases using a text mining tool is very low, despite the well-established good performance of the tool and even when the full text of the associated article is available for processing. We demonstrate that this discrepancy can be explained by considering the supplementary material linked to the published articles, not previously considered by text mining tools. Although it is anecdotally known that supplementary material contains ‘all of the information’, and some researchers have speculated about the role of supplementary material (Schenck et al. Extraction of genetic mutations associated with cancer from public literature. J Health Med Inform 2012;S2:2.), our analysis substantiates the significant extent to which this material is critical. Our results highlight the need for literature mining tools to consider not only the narrative content of a publication but also the full set of material related to a publication.

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Section: Discussionsupporting

confidence: 90%

Literature mining of genetic variants for curation: quantifying the importance of supplementary material

Jimeno-Yepes

Verspoor

2014

Database

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“…The Mutator tool (7) uses regular expressions to recognize mutations and was tested on mutations related to Fabry disease. The LEAP-FS system aims to recognize all protein amino acid mentions in text, including mutations but also bare mentions (29), and subsequent work with that tool addresses identifying relations between residues and their associated proteins in text (30) as well as functional classification of those residues as catalytic (31). …”

Section: Discussionmentioning

confidence: 99%

Annotating the biomedical literature for the human variome

et al. 2013

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This article introduces the Variome Annotation Schema, a schema that aims to capture the core concepts and relations relevant to cataloguing and interpreting human genetic variation and its relationship to disease, as described in the published literature. The schema was inspired by the needs of the database curators of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) database, but is intended to have application to genetic variation information in a range of diseases. The schema has been applied to a small corpus of full text journal publications on the subject of inherited colorectal cancer. We show that the inter-annotator agreement on annotation of this corpus ranges from 0.78 to 0.95 F-score across different entity types when exact matching is measured, and improves to a minimum F-score of 0.87 when boundary matching is relaxed. Relations show more variability in agreement, but several are reliable, with the highest, cohort-has-size, reaching 0.90 F-score. We also explore the relevance of the schema to the InSiGHT database curation process. The schema and the corpus represent an important new resource for the development of text mining solutions that address relationships among patient cohorts, disease and genetic variation, and therefore, we also discuss the role text mining might play in the curation of information related to the human variome. The corpus is available at http://opennicta.com/home/health/variome.

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“…Although we did not attempt to establish the specific nature of the relationship between the SNP and the gene as mentioned in the article, prior work has found that simple co-occurrence of such concepts can be useful to establish a biological relationship (Gabow et al, 2008; Verspoor et al, 2013; Sokolov et al, 2013). …”

Section: Methodsmentioning

confidence: 99%

Associating disease-related genetic variants in intergenic regions to the genes they impact

Macintyre

Jimeno-Yepes

Ong

et al. 2014

PeerJ

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We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available, this method provides a way forward towards functional interpretation of SNPs in the context of the three dimensional structure of the genome in the nucleus.

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Detection of Protein Catalytic Sites in the Biomedical Literature

Cited by 7 publications

References 15 publications

Literature mining of genetic variants for curation: quantifying the importance of supplementary material

Literature mining of genetic variants for curation: quantifying the importance of supplementary material

Annotating the biomedical literature for the human variome

Associating disease-related genetic variants in intergenic regions to the genes they impact

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