BioCreative III interactive task: an overview.

Background: The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of biomedical literature, provides a diverse and engaged end user group for text mining tools. Earlier BioCreative challenges involved many text mining teams in developing basic capabilities relevant to biological curation, but they did not address the issues of system usage, insertion into the workflow and adoption by curators.

The gene normalization task in BioCreative III.

Background: We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 fully and 500 partially annotated articles were prepared. A total of 507 articles were selected as the test set.

Building a high-quality sense inventory for improved abbreviation disambiguation.

Motivation: The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations.

Secoiridoid glucosides and unusual recyclized secoiridoid aglycones from Ligustrum vulgare.

Phytochemical investigation of the dried leaves and twigs of Ligustrum vulgare has led to the isolation of the secoiridoid glucosides, (2''R)- and (2''S)-10-hydroxy-2''-methoxyoleuropeins (1 and 2), and the secoiridoid aglycones, ligustrohemiacetals A (3) and B (4). Their structures were elucidated by spectroscopic and chemical means. Enzymatic hydrolysis of 10-hydroxyoleuropein to the analog of ligustrohemiacetals A and B led to the structural revision of jasmolactones.

Building an abbreviation dictionary using a term recognition approach.

Motivation: Acronyms result from a highly productive type of term variation and trigger the need for an acronym dictionary to establish associations between acronyms and their expanded forms.

Results: We propose a novel method for recognizing acronym definitions in a text collection. Assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form, our method identifies acronym definitions in a similar manner to the statistical term recognition task.

Secoiridoid and iridoid glucosides from Syringa afghanica.

Phytochemical investigation of the dried leaves of Syringa afghanica, has led to the isolation of nine secoiridoid glucosides, safghanosides A-H and 2"-epi-frameroside, as well as an iridoid glucoside, syringafghanoside along with nineteen known compounds. The structures were elucidated by spectroscopic and chemical means.