A Structured Digital Abstract (SDA) is a method of describing relationships between biological entities in a structured, but human-readable, format. It is added below the abstract of scientific articles published in

FEBS Letters ''FEBS Letters'' is a not-for-profit peer-reviewed scientific journal published on behalf of the Federation of European Biochemical Societies (FEBS) by Wiley. It covers all aspects of molecular biosciences, including molecular biology and bioc ...

and

FEBS Journal ''The FEBS Journal'' is a biweekly peer-reviewed scientific journal published by John Wiley & Sons on behalf of the Federation of European Biochemical Societies. It covers research on all aspects of biochemistry, molecular biology, cell biology, an ...

. Current SDAs describe protein-protein interactions.

History

Many scientific manuscripts describe relationships between entities such as

genes In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

and

proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respondi ...

. However, this information cannot be used efficiently because of the difficulties in retrieving it automatically from unstructured text.Finally: The digital, democratic age of scientific abstracts, Giulio Superti-Furga, Felix Wieland and Giovanni Cesareni, ''FEBS Lett'' (2009) 582, 1169 In a six-month pilot project that started in January 2008,

began publishing manuscripts with “structured digital abstracts” (SDAs). The SDAs were added to the end of abstracts in a structured, but human-readable, format and digitally linked to interaction databases. In the pilot project, the journal concentrated on protein-protein interactions. After six months, this “experiment” was evaluated. As it was a success, all appropriate

manuscripts are now given an SDA. In 2009,

also started publishing manuscripts with SDAs. The SDA initiative continues to be funded by

FEBS The Federation of the European Biochemical Societies, frequently abbreviated FEBS, is an international scientific society promoting activities in biochemistry, molecular biology and related research areas in Europe and neighbouring regions. It was f ...

, a not-for-profit organisation. Recent

BioCreative BioCreAtIvE (A critical assessment of text mining methods in molecular biology) consists in a community-wide effort for evaluating information extraction and text mining developments in the biological domain. It was preceded by the Knowledge Disco ...

challenges have focused on protein-protein interaction extraction by automatic

text mining Text mining, also referred to as ''text data mining'', similar to text analytics, is the process of deriving high-quality information from text. It involves "the discovery by computer of new, previously unknown information, by automatically extract ...

, using

and

articles.

Format

An SDA comprises a series of sentences each of which contains a relationship between two biological entities, mentioning the method used to study the relationship. To provide a simplified example:

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...

A interacts with

B, by method X. Each sentence in an SDA is followed by one or more identifiers pointing to the corresponding database entries that contain all the details of the structured information. Although most of the sentences currently point to th
MINT Molecular INTeraction Database
the proposed structure can easily be extended to contain identifiers from other databases storing protein interactions or different types of relationships between biological entities. Each entity is also linked to the appropriate explanatory database. e.g.

UniProtKB UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from ...

for proteins and the

European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the We ...

ontology look up service for other entities.

References

Molecular and cellular biology journals {{Molec-cell-biology-journal-stub