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. 2021 Oct 23;22(1):517.
doi: 10.1186/s12859-021-04429-5.

TAGOPSIN: collating taxa-specific gene and protein functional and structural information

Eshan Bundhoo #  1 , Anisah W Ghoorah #  2 , Yasmina Jaufeerally-Fakim  1
Affiliations

TAGOPSIN: collating taxa-specific gene and protein functional and structural information

Eshan Bundhoo et al. BMC Bioinformatics. .

Abstract

Background: The wealth of biological information available nowadays in public databases has triggered an unprecedented rise in multi-database search and data retrieval for obtaining detailed information about key functional and structural entities. This concerns investigations ranging from gene or genome analysis to protein structural analysis. However, the retrieval of interconnected data from a number of different databases is very often done repeatedly in an unsystematic way.

Results: Here, we present TAxonomy, Gene, Ontology, Protein, Structure INtegrated (TAGOPSIN), a command line program written in Java for rapid and systematic retrieval of select data from seven of the most popular public biological databases relevant to comparative genomics and protein structure studies. The program allows a user to retrieve organism-centred data and assemble them in a single data warehouse which constitutes a useful resource for several biological applications. TAGOPSIN was tested with a number of organisms encompassing eukaryotes, prokaryotes and viruses. For example, it successfully integrated data for about 17,000 UniProt entries of Homo sapiens and 21 UniProt entries of human coronavirus.

Conclusion: TAGOPSIN demonstrates efficient data integration whereby manipulation of interconnected data is more convenient than doing multi-database queries. The program facilitates for instance interspecific comparative analyses of protein-coding genes in a molecular evolutionary study, or identification of taxa-specific protein domains and three-dimensional structures. TAGOPSIN is available as a JAR file at https://github.com/ebundhoo/TAGOPSIN and is released under the GNU General Public License.

Keywords: Comparative genomics; Data integration; Data retrieval; Database; Object-oriented biology.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The data model of TAGOPSIN, represented as an ERD
Fig. 2
Fig. 2
Relational database schema representing schematically the data warehouse built by TAGOPSIN. Primary key (PK) attributes (allowing unique identification) are in bold and underlined. An arbitrary PK was chosen where a satisfactory biological attribute could not symbolize it (e.g. OID, CDS ID, NTS ID). Foreign key attributes are indicated by (FK). Arrows indicate how one relation is linked to another. Start, Stop: start and end positions on the corresponding sequence; SP Start, SP Stop: start and end positions on the Swiss-Prot sequence; PDB Start, PDB Stop: start and end positions on the PDB structure
Fig. 3
Fig. 3
Sequential steps in the functioning of TAGOPSIN
Fig. 4
Fig. 4
Class diagram illustrating the data model of TAGOPSIN
See this image and copyright information in PMC

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