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."
NOTE TO AUTHORS:
Authors of protein-protein interaction papers are encouraged at acceptance to fill in a spreadsheet for data submission - see also the MINT website.
The Molecular INTeraction database (MINT, http://mint.bio.uniroma2.it/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 (http://imex.sourceforge.net/) to share curation efforts and supports the Protein Standard Initiative (PSI) recommendations.
The Molecular Interaction (MI) Controlled Vocabulary provides a means to describe the relationship between two molecules, either described experimentally or predicted using an appropriate algorithm. The methods by which an interaction has been defined, the properties of a molecule enabling the interaction and the type and directionality of the interaction may be depicted in an unambiguous manner, according to the definition of the terms used. The ontology may be viewed in full, or an individual term searched, using the Ontology Lookup Service available at www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI. |
