FEBS Letters Structured Digital Abstracts Experiment
Protein interaction papers to have Structured Digital Summary
Amsterdam, 2 April 2008 - FEBS Letters, one of the leading journals for short reports in molecular biosciences, announced today an exciting new enhancement to the journal article: Structured Digital Abstracts (SDA).
A Structured Digital Abstract in FEBS Letters is an extension of the regular journal article abstract comprising of a series of sentences each of which contains a relationship between two biological entities, mentioning the method used to study the relationship. Each sentence is preceded by one or more identifiers pointing to the corresponding database entries that contain the full details of the interaction. To provide a simplified example of a potential relationship: protein A interacts with protein B, by method X.
A Special Issue of FEBS Letters, Volume 582/8 (9 April) marks the launch of Structured Digital Abstracts and explains the experiment and relevance in full detail.
The aim of the experiment is threefold:
• To develop and fine tune simple tools to facilitate data entries and the authors selection of terms from controlled vocabularies.
• To propose a text layout for a structured abstract to be appended to the traditional abstract.
• To investigate and estimate the authors’ degree of interest (and competence) in a project implicating them as active players in this “editorial revolution”.
This innovative experiment is a joint project between the curators of the MINT Molecular Interactions database in Rome, the FEBS Letters Editorial Office in Heidelberg, and leading global experts in text- mining and bioinformatics.
As Gianni Cesareni, Editor of FEBS Letters and in charge of the MINT database explains: “Many articles in biological journals describe relationships between entities (genes, proteins, etc.) yet this information cannot be efficiently used because of difficulties in retrieving from text. Databases capture this valuable information and organize it in a structured format ready for automatic analysis. The experiment of using SDAs will facilitate database entry and improve disclosure, to the benefit of authors and readers.”
In the FEBS Letters special issue Florian Leitner and Alfonso Valencia propose that a combination of human expertise and automatic text-mining systems can be used to create a first generation of electronically annotated information that can be added to journal abstracts and that is directly related to the information in the corresponding text.
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The Federation of European Biochemical Societies (FEBS), since its inception in 1964, has promoted life sciences and supported scientists in Europe and elsewhere, and is one of the largest not-for-profit organizations in life sciences today. FEBS offers its members advanced courses, fellowships and participation in their annual Congress. All activities related to FEBS are financed by income generated by their three publications: FEBS Letters, FEBS Journal and Molecular Oncology. Their mission is to foster scientific excellence and promote science for society.
The Molecular INTeraction database ( MINT) aims at storing, in a structured format, information about molecular interactions (MIs) by extracting experimental details from work published in peer-reviewed journals. At present the MINT team focuses the curation work on physical interactions between proteins. Over the past few years the number of curated physical interactions has soared to over 95 000. MINT now includes, as an integrated addition, HomoMINT, a database of interactions between human proteins inferred from experiments with ortholog proteins in model organisms.
MINT has signed the iMEX agreement to share curation efforts and supports the Protein Standard Initiative (PSI) recommendations.About Elsevier
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