Orphans make sense

Discovering Biomedical Semantic Relations in PubMed Queries for Database Curation and Literature Retrieval

Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.

We demonstrate that annotation removal or reassignment is rarely linked to incorrect annotation by the curator, but are necessitated by both changes in the underlying data and improved published scientific knowledge

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glycans

is moving towards a more expressive way of describing the function of gene products

hniques. In creating PolySearch2's list of system filter words, we tagged the occurrence of all b

convert PolySearch2 from a simple association discovery tool to a more general knowledge extraction tool.

users may indicate certain associations to be false positives and in subsequent runs PolySearch2 should ideally learn from these negative examples and adapt itself to match a user's specific search needs and thereby achieve higher accuracy

The improvement in association accuracy can be attributed to the tightness measure we introduced to further discriminate matched association patterns, the assignment of weight boosting to database records in contrast to text articles and the imposition of more stringent cut-offs to boost precision at the expense of recall (precision-recall trade-off).

PolySearch2 achieved a 3–12% improvement in its association accuracy.

PolySearch2's f-measures in these tasks were 88.95, 89.75, 93.79 and 90.74,

All of these thesauri may be searched via PolySearch2's Thesaurus page, and all may be downloaded via PolySearch2's Download page

PolySearch2, we have significantly expanded the number of thesauri from 9 to 20 categories, and from just 57 706 terms to over 1.13 million term entries with more than 2.84 million synonyms.

Figure 1

raw relevancy score (see (7))

empirically determined ‘weight boost’

improves the scoring of co-occurrences and enhances PolySearch2's ability to distinguish genuine associations from incidental co-occurrences that arise by chance

key limitation with PolySearch has been the long search times (2–3 min), its limited synonym set (thesauri) and its relatively small number of searchable databases

disease–gene discovery (13,14), protein–protein interaction studies (15,16), microarray data analysis (17), metabolome annotation (9,11,12,18), biomarker discovery (19), as well as in building and assessing other biomedical text-mining tools (20,21).

free-text collections

Given X, find all associated Ys

Our results showed that the f-measure for PolySearch alone was 70.2, the f-measure for PolySearch with its GAD and OMIM options turned on was 78.5, the f-measure for EBIMed was 66.0, the f-measure for LitMiner was 5.8 and for GAD it was 27.5

A text mining tool is only useful if it gives accurate results and extensive coverage in less time than what could be performed using alternative (i.e. non-computational) or competing computational methods.

automated genome analysis pipelines

massive