Post on 18-Dec-2015
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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
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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
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ERMSERMS
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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)
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How many species?How many species?
About 29,500
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ERMS geographical areaERMS geographical area
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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
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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)
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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
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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
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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
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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
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“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::::
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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)
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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)
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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.
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