Another Word For It Patrick Durusau on Topic Maps and Semantic Diversity

November 26, 2012

Collaborative biocuration… [Pre-Topic Map Tasks]

Filed under: Authoring Topic Maps,Bioinformatics,Biomedical,Curation,Genomics,Searching — Patrick Durusau @ 9:22 am

Collaborative biocuration—text-mining development task for document prioritization for curation by Thomas C. Wiegers, Allan Peter Davis and Carolyn J. Mattingly. (Database (2012) 2012 : bas037 doi: 10.1093/database/bas037)

Abstract:

The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems for the biological domain. The ‘BioCreative Workshop 2012’ subcommittee identified three areas, or tracks, that comprised independent, but complementary aspects of data curation in which they sought community input: literature triage (Track I); curation workflow (Track II) and text mining/natural language processing (NLP) systems (Track III). Track I participants were invited to develop tools or systems that would effectively triage and prioritize articles for curation and present results in a prototype web interface. Training and test datasets were derived from the Comparative Toxicogenomics Database (CTD; http://ctdbase.org) and consisted of manuscripts from which chemical–gene–disease data were manually curated. A total of seven groups participated in Track I. For the triage component, the effectiveness of participant systems was measured by aggregate gene, disease and chemical ‘named-entity recognition’ (NER) across articles; the effectiveness of ‘information retrieval’ (IR) was also measured based on ‘mean average precision’ (MAP). Top recall scores for gene, disease and chemical NER were 49, 65 and 82%, respectively; the top MAP score was 80%. Each participating group also developed a prototype web interface; these interfaces were evaluated based on functionality and ease-of-use by CTD’s biocuration project manager. In this article, we present a detailed description of the challenge and a summary of the results.

The results:

“Top recall scores for gene, disease and chemical NER were 49, 65 and 82%, respectively; the top MAP score was 80%.”

indicate there is plenty of room for improvement. Perhaps even commercially viable improvement.

In hindsight, not talking about how to make a topic map along with ISO 13250, may have been a mistake. Even admitting there are multiple ways to get there, a technical report outlining one or two ways would have made the process more transparent.

Answering the question: “What can you say with a topic map?” with “Anything you want.” was, a truthful answer but not a helpful one.

I should try to crib something from one of those “how to write a research paper” guides. I haven’t looked at one in years but the process is remarkably similar to what would result in a topic map.

Some of the mechanics are different but the underlying intellectual process is quite similar. Everyone who has been to college (at least of my age), had a course that talked about writing research papers. So it should be familiar terminology.

Thoughts/suggestions?

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