Event

February 24-27, 2013 Bethesda, Maryland

Genomic Sciences Program (GSP) 2013

Contractors-Grantees Meeting XI
This Extended KWIC (Key Word In Context) Index incorporates several new software components developed during this project. This application is used to rapidly identify candidate terms for the ontology and investigate their usage in the taxonomic literature. In the above screenshot, we see that the descriptions of 376 type strains contain occurrences of “methyl α-d-glucoside”. A curator can scan through each description in the taxonomic literature to collect examples that demonstrate every usage variation of that term (e.g. “acid production from”, “no acid production from”, “ferments”, “does not ferment”).
This Extended KWIC (Key Word In Context) Index incorporates several new software components developed during this project. This application is used to rapidly identify candidate terms for the ontology and investigate their usage in the taxonomic literature. In the above screenshot, we see that the descriptions of 376 type strains contain occurrences of “methyl α-d-glucoside”. A curator can scan through each description in the taxonomic literature to collect examples that demonstrate every usage variation of that term (e.g. “acid production from”, “no acid production from”, “ferments”, “does not ferment”).

Charles Parker and George Garrity will be presenting a poster (“The NamesforLife Semantic Index of Phenotypic and Genotypic Data”) during the evening mixers (5:00pm-7:00pm) on Monday and Tuesday. We will be highlighting our team’s recent research on Information Extraction (IE) and automated thesaurus construction.

Please note that due to federal travel restrictions, this meeting’s attendance and scope will be limited, and no abstracts document will be published. We appreciate the folks from Oak Ridge National Labs, who took a bus all the way from Tennessee to attend this meeting!

Phenotypic data needs to be viewed from an historical perspective to understand not only what was measured but how it was measured (growth on substrate vs. hydrolysis of indicator compound). It is also important to know which methods were applied and whether different methods within an array of data are measuring the same trait, and if so, whether the results are comparable.

The Phenotypic Index will address these issues by tying together observations under specific sets of growth conditions, supporting faceted search, retrieval and comparison of differentiating characteristics between (and within) taxonomic groups. Each phenotypic observation will be linked to a strain via a NamesforLife Exemplar DOI (Digital Object Identifier), which is directly linked to an actively maintained taxonomy and nomenclature.

Parker et al., “The NamesforLife Semantic Index of Phenotypic and Genotypic Data”

Download Poster (630kB PDF)

[permalink] Posted February 24, 2013.

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