The EMBL/EBI Reptile Database

Several million species inhabit the earth. Among them are about 8000 reptiles and about 5000 amphibians. Several attempts have been made to put some order into this vast diversity, most notably by the series "Das Tierreich" which was published originally by the German Zoological Society. Apart from listing all animal species, the "Tierreich" also aimed at listing all synonyms for a given taxon, an indispensable task in order to avoid complete confusion among the several scientific names most species have receiced since their first description. For example, the recent list of Australian and oceanian geckos by Bauer (1994) revealed more than 800 different names for about 170 geckos of this region!

A comprehensive taxonomy of reptiles and amphibians is the basis for both systematical and all other aspects of herpetology as well as herpetoculture, hence it should be widely available and up to date. In contrast to books and journals these two criteria are only met by electronic databases on the internet. To our knowledge there is no online-database on reptile species available so far. The only comprehensive internet database on vertebrate species to date is an online-version of the venerable "Mammal species of the World" (Wilson & Reeder, 1993) [note added on April 2, 1997: W. E. Eschmeyer et al. recently put their fish database on the web as well]. For this reason we set up a prototype database which is based on the Sequence Retrieval System (SRS), originally developed for the access of DNA and protein sequence data over the internet (Etzold et al. 1996).

The aim of the database is the collection of taxonomic data on all living reptiles. For this purpose the database is split into two parts, a species database and a database on higher taxa. Currently the species database contains about 7600 species, of which about 6300 have some information on distribution associated. More than 3000 species entries contain references to more detailed information (including pictures). An entry consists of six different data fields (fig. 1):

Fig. 1 species sample entry

Species:
          Vipera monticola
   Synonyms:
          1953 Vipera latastei montana Saint Girons 
       1954 Vipera latastei monticola Saint Girons
   Subspecies:
Distribution:
          Morocco (Haut Atlas)
   Comment:
References:
          Schleich,H.H., Kästle,W., Kabisch, K. (1996)
       Amphibians and Reptiles of North Africa
       Koeltz, Koenigstein, 627 pp. 

The species entries currently do not contain much information apart from some data on the distribution of particular species. Hence, we welcome submission of such data (including detailed descriptions) from the herpetological community. For the time being, only data that have been published regularly will be entered until a scientific advisory board has been established that might review direct submissions (for comments on copyright issues see our web page). Technically, it is no problem to include pictures and distribution maps as well, although the short-term goal of the database is a text-based catalog of all reptile taxa.

Entries of the higher taxa database (fig. 2) are similar to the species entries:

Fig. 2 higher taxon sample entry

ID:
Taxon:
     Tropidurinae
   Synonyms:
     1843 Tropidurinae Bell
  1843 Ptychosauri Fitzinger
  1843 Steirolepides Fitzinger
  1843 Heterotropides Fitzinger
   Category:
     Subfamily
   Up:
     Tropiduridae
   Status:
     valid
   Description:
     premaxillary spine not overlapped by nasals
  parietal table not Y- or V-shaped
  no labial blade or coronoid
  splenial extending anteriorly no more than 1/6 length of precoronoid 
      length of mandible
  anterior process of interclavicle poorly developed or absent
  interparietal scale enlarged
  no preanal pores
  nasal concha fused to roof of nasal chamber
  nasal vestibule relatively short and straight
  bisulcate, weakly to strongly bicapitate hemipenes
   Comment:
     Bell's Tropiduridae seems to have priority over Fitzingers Steirolepides, 
  Ptychosauri, and Heterotropides
   Reference:
     Frost,D.E. & Etheridge,R.E. (1989)
  A Phylogenetic Analysis and Taxonomy of Iguanian Lizards (Reptilia: Squamata)
  Univ. Kansas Mus. Nat. Hist. Misc. Publ. 81
   //

The higher taxon database is currently under development and not yet available to the public. We expect release in January 1997 [note added on April 3, 1997: the higher taxon database is indeed available. Check the "Databank" list on the database SEARCH form. However, since nobody provided any material so far, we don't work on this database currently and haven't written any documentation yet. The sample entry given above just serves to illustrate the general structure of such a database]. It will allow automatic reconstruction of taxonomic hierarchies by means of the "Up" data field, i.e. all lower taxa of a family or higher taxa pertaining to a species.

For instance, it will allow retrieval of all species of a particular taxon. The database can be accessed easily on the World Wide Web. A form allows for quick searching of different data fields (like species, e.g. species or genera like "Testudo" or "Testudo hermanni" or distribution like "Mexico" or "Chiapas"). Logical combinations are possible (e.g. "Tantilla" OR "Coluber" combined with "USA" OR "Mexico" searches for all Tantilla and Coluber species in both Mexico and the USA.

Alternatively, the database can be browsed via hierarchically organized web pages starting with a taxonomic overview (subclasses, orders, suborders). From there, infraorders/superfamilies, families and genera can be accessed. Clicking on single genera eventually activates the search engine and retrieves all species of a particular genus.

A major advantage of the SRS system is it's ability to be linked to other databases. So far, we implemented a link to the GenBank DNA sequence database. Thereby, it is possible to search for all species of, say, Anolis and list all available sequence data alongside. In the future it is expected that other areas of biology will be made available as databases as well. It is well conceivable that databases of taxonomy and molecular biology, and eventually of morphology, ethology, and other disciplines will be flexibly intertwined as they deserve from a biological viewpoint.

In the long run, newly described species should be entered into the database in addition to be published regularly. Similar to molecular biology journals we encourage herpetological journals to adopt a policy requiring parallel submission of manuscripts to the journal and primary data to the database (note that many molecular biology journals do not print DNA sequence data anymore but refer readers to an accession number in a public DNA database). For instance, the Herpetological Review might ask authors for submission of new distribution data to the database before publication. The database would then also serve as a public repository for all these data.

The database should be considered as an experiment for the time being. We are well aware of the fact that the data are incomplete, outdated or even wrong. The success and usability therefore depends on the contributions of external experts. In particular, we are looking for interested specialists serving as coordinators (or "reviewers") for higher taxa. Detailed information for contributors may be found on our webpage.

Acknowledgements

We are in great debt to people who provided species lists or other information, in particular Petr Necas (Chamaeleonidae), Klaus Adolphs (Gerrhosauridae, Cordylidae), Wolfgang Bischoff (Lacertidae), Adam Britton (Crocodylia).

The EBI Reptile database: http://www.embl-heidelberg.de/~uetz/LivingReptiles.html [now inactive; new URL: http://www.reptile-database.org/]

References:

Bauer,A.M. (1994) Gekkonidae (Reptilia, Sauria) Das Tierreich Bd. 109, Part I (Australia and Oceania), Walter de Gruyter, Berlin, 1-306

Etzold,T. Ulyanov,A. & Argos,P. (1996) SRS: Information Retrieval Systems for Molecular Biology Data Banks. Meth. Enzymol. 266: 114-128

Wilson, D. E., and D. M. Reeder, eds. (1993) Mammal Species of the World. Smithsonian Institution Press, 1206 pp.

This article has been originally published in Herpetological Review 27 (4): 174-175 (1996)

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