Taxonomy applied to sequence data

Una Smith una at MINERVA.CIS.YALE.EDU
Mon Oct 25 17:46:47 CDT 1993


This article from bionet.general may be of interest to TAXACOM readers.
The sequence database projects are trying to build a "unified" taxonomic
system for use in accessioning and retrieving sequences.

        Una

-----------------------------------------------------------------------------

                    The NCBI Taxonomy Project

We were very happy to receive over fifty positive responses to the
posting about the NCBI Taxonomy Project. We would, however, like to
clarify the sources of data to the project and, in particular, to
acknowledge the premier contribution of the PIR-International taxonomy
maintained by Andrzej Elzanowski, MIPS am Max-Planck-Institut fuer Biochemie,
Martinsried, Germany. The work performed at the PIR-International is,
in our opinion, of the highest biological content and quality. The
PIR-International is the only one of the sequence databases that has
employed a taxonomist to maintain their taxonomy.

We are indebted to the work done by other sequence database groups
(SwissProt, GenBank, EMBL, and DDBJ) as well as taxonomic databases from
other sources (the ICTV virus taxonomy, the USDA plant taxonomy, and the
Drosophilidae taxonomy from the FlyBase project). We want to ensure that
their contributions are publicly acknowledged here, and have detailed
our use of these sources consistently in the text documents posted at our
FTP site (repository/taxonomies/taxman at ncbi.nlm.nih.gov).

We have used the PIR-International taxonomy as the starting point for
our merged view of the sequence database taxonomies. The other sequence
database taxonomies (GenBank, EMBL, DDBJ and SwissProt) were used for
the next rounds of the taxonomy merging process.

Where we have found international standard taxonomic databases (for example,
the ICTV taxonomy) appropriate to our particular needs as maintainers of the
GenBank sequence database, we have substituted these taxonomies at the
appropriate branches of the tree in our merged view of the sequence database
taxonomy.

We gratefully acknowledge the contributions from all of these sources, and
look forward to a continuing collaboration with these (and other) parties
in our effort to produce consistent views of the taxonomy that will span
the various sequence databases.

Please send comments & criticisms to:

Scott federhen at ncbi.nlm.nih.gov

-----------------------------------------------------------------------------




More information about the Taxacom mailing list