Http://erms.biol.soton.ac.uk Building the European Register of Marine Species Richard White...

http://erms.biol.soton.ac.uk

Building the European Register of Marine Species

Richard WhiteBiodiversity & Ecology Research Division, School of Biological Sciences, University of Southampton, UK

Mark Costello & Chris EmblowEcological Consultancy Services Ltd (EcoServe),Dublin, Ireland


European Register of Marine Species (ERMS)European Register of Marine Species (ERMS)

Funded as a Concerted Action project by the MAST (Marine Science and Technology) programme of the European Union

Managed by EcoServe in DublinTeam of participants including “list

editors”http://erms.biol.soton.ac.uk


ERMSERMS


ERMS versus URMOERMS versus URMO

URMO is creating global lists of marine organisms but is not taxonomically complete

ERMS is creating a regional list (for European waters) but it is (almost) taxonomically complete

With the Fauna Europaea and Euro+Med PlantBase projects, Europe will have a complete list of its species (almost)


How many species?How many species?

About 29,500


ERMS geographical areaERMS geographical area


Incoming dataIncoming data

Approximately 100 separate lists for different taxonomic groups

Mostly compiled as spreadsheetsScientific names, synonyms, geography

(at least Atlantic or Mediterranean)Some optional fields


List conversionList conversion

is carried out in several stages: Excel spreadsheets are exported to text files Tab-delimited text files are converted to

“holding format” (was XDF, now a client-server database (MySQL)

Database queries results are passed through templates to generate either RTF (for the printed publication) or HTML (for the Web site)


Data flowData flow

(was “temporarydata”)

Transferformat

Listproducer

Transferformat

Listproducer

Experts

Literature

Transferformat

Database

Transferformat

Database

(was “core archive”)

Holdingformat

CD-Rom Reports

Web site

Possible direct editing


Variations on a themeVariations on a theme Fields may be combined or separated

e.g. genus species authority date Higher taxa may be:

repeated in fields of the species record given once in separate preceding records in various

different formats Synonyms may be:

in a separate field of the species record, or mixed with other remarks, with various delimiters and separators

in separate records, linked by code or by name or even abbreviated

implied, e.g. Genus1 specname (Smith as Genus2) Geographical information is often free text


Conversion: simple caseConversion: simple case

#!/usr/bin/perl -w

# Porifera.pl: convert an ERMS list text file to an XDF file

use PerlStart; use ERMS;

&speciesList();

__END__

list code PF

list version 1

list rank phylum

record 1 fields

field 1 genus

field 2 species

field 3 species authority and date

field 4 used


More complicated caseMore complicated case#!/usr/bin/perl -w

# Tardigrada.pl: convert an ERMS list text file to an XDF file

use PerlStart; use ERMS;

&speciesList ( sub { &extractSynonyms(10, "syn.:"); } );

__END__

list code TG

list version 2

list rank phylum

record 1 title

record 2 fields

field 1 order

field 2 family

field 3 genus

field 4 species

field 5 subspecies

field 6 species authority

field 7 species date

field 8 geography

field 9 reference

field 10 remarks


“Holding format” XDF file“Holding format” XDF file

(HIGHER:informal:Tetrapoda)

(HIGHER:order:Testudines)

(HIGHER:family:Cheloniidae)

TP00001:Caretta:caretta:(Linnaeus, 1758):species::::::::Cosmopolitan warm to temperate waters::::Loggerhead turtle::::

TP00002:Chelonia:mydas:(Linnaeus, 1758):species::::::::Cosmopolitan warm water::::Green turtle::::

TP00003:Eretmochelys:imbricata:(Linnaeus, 1766):species::::::::Cosmopolitan warm water::::Hawksbill turtle::::


Example RTF file for the bookExample RTF file for the book

Order Isopoda

Suborder Anthuridea

Family Antheluridae

Ananthuraabyssorum (Norman & Stebbing, 1886) A

Antheluraelongata Norman & Stebbing, 1886 A

ovalis (Barnard, 1925) M

= Ananthura ovalis

sulcaticauda (Barnard, 1925) A

= Ananthura sulcaticauda

truncata (Hansen, 1916)


Static versus dynamic web pagesStatic versus dynamic web pages

Initial web pages were generated statically (in advance) from the XDF “holding format” (without synonyms)

RTF files were generated from the database (with synonyms)

Future web pages will be generated dynamically (on demand) from the database (with synonyms)


Database schema (simplified)Database schema (simplified)

Taxon file: Name table:taxon ID (PK) name ID (PK)geography taxon ID (I, FK)etc. Genus (I,

FK)species (I)

Hierarchy table: authortaxon (PK) etc.rankparent (I, FK)etc.

Http://erms.biol.soton.ac.uk Building the European Register of Marine Species Richard White...

Documents

Transcript of Http://erms.biol.soton.ac.uk Building the European Register of Marine Species Richard White...