Structured digital abstract
Encyclopedia
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
and FEBS Journal
. Current SDAs describe protein-protein interactions.
[File:SDA_logo_yellow_shadow.jpg]
and proteins. However, this information cannot be used efficiently because of the difficulties in retrieving it automatically from unstructured text. In a six-month pilot project that started in January 2008, FEBS Letters
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 FEBS Letters
manuscripts are now given an SDA.
In 2009, FEBS Journal
also started publishing manuscripts with SDAs.
The SDA initiative continues to be funded by FEBS, a not-for-profit organisation.
Recent BioCreative
challenges have focused on protein-protein interaction
extraction by automatic text mining
, using FEBS Letters
and FEBS Journal
articles.
A interacts with protein
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 the 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 for proteins and the European Bioinformatics Institute
ontology look up service for other entities.
FEBS Letters
FEBS Letters is a peer-reviewed scientific journal covering all aspects of biochemistry. The journal publishes minireviews, hypotheses, and research letters. FEBS Letters is one of two journals published by Elsevier for the Federation of European Biochemical Societies , along with Molecular...
and FEBS Journal
FEBS Journal
FEBS Journal is a scientific journal published by the Federation of European Biochemical Societies . Before 2005, this journal was known as the European Journal of Biochemistry, which itself was the new name of Biochemische Zeitschrift that was adopted in 1967...
. Current SDAs describe protein-protein interactions.
[File:SDA_logo_yellow_shadow.jpg]
History
Many scientific manuscripts describe relationships between entities such as genesGênes
Gênes is the name of a département of the First French Empire in present Italy, named after the city of Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa. Its capital was Genoa, and it was divided in the arrondissements of Genoa, Bobbio, Novi Ligure, Tortona and...
and proteins. However, this information cannot be used efficiently because of the difficulties in retrieving it automatically from unstructured text. In a six-month pilot project that started in January 2008, FEBS Letters
FEBS Letters
FEBS Letters is a peer-reviewed scientific journal covering all aspects of biochemistry. The journal publishes minireviews, hypotheses, and research letters. FEBS Letters is one of two journals published by Elsevier for the Federation of European Biochemical Societies , along with Molecular...
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 FEBS Letters
FEBS Letters
FEBS Letters is a peer-reviewed scientific journal covering all aspects of biochemistry. The journal publishes minireviews, hypotheses, and research letters. FEBS Letters is one of two journals published by Elsevier for the Federation of European Biochemical Societies , along with Molecular...
manuscripts are now given an SDA.
In 2009, FEBS Journal
FEBS Journal
FEBS Journal is a scientific journal published by the Federation of European Biochemical Societies . Before 2005, this journal was known as the European Journal of Biochemistry, which itself was the new name of Biochemische Zeitschrift that was adopted in 1967...
also started publishing manuscripts with SDAs.
The SDA initiative continues to be funded by FEBS, a not-for-profit organisation.
Recent BioCreative
BioCreative
BioCreAtIvE consists in a community-wide effort for evaluating information extraction and text mining developments in the biological domain....
challenges have focused on protein-protein interaction
Protein-protein interaction
Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. Many of the most important molecular processes in the cell such as DNA replication are carried out by large molecular machines that are built from a large number of protein...
extraction by automatic text mining
Text mining
Text mining, sometimes alternately referred to as text data mining, roughly equivalent to text analytics, refers to the process of deriving high-quality information from text. High-quality information is typically derived through the devising of patterns and trends through means such as...
, using FEBS Letters
FEBS Letters
FEBS Letters is a peer-reviewed scientific journal covering all aspects of biochemistry. The journal publishes minireviews, hypotheses, and research letters. FEBS Letters is one of two journals published by Elsevier for the Federation of European Biochemical Societies , along with Molecular...
and FEBS Journal
FEBS Journal
FEBS Journal is a scientific journal published by the Federation of European Biochemical Societies . Before 2005, this journal was known as the European Journal of Biochemistry, which itself was the new name of Biochemische Zeitschrift that was adopted in 1967...
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: proteinProtein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
A interacts with protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
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 the 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 for proteins and the European Bioinformatics Institute
European Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
ontology look up service for other entities.