WoRMS System Description

Ward Appeltans

Version 16 June 2008

The WoRMS database system

Background

Description of database

Users

Data progress

Special collections

Editing, rights and data quality

Future developments

How to retrieve information from the database

Through the website

Through the download page

Through the taxon match tool

Through the webservice

Through RSS feeds

How to add information to the database

Add a new valid taxon

Add a new invalid taxon

Add a an environment flag

Add a new source

Add a source to a taxon

Add a new vernacular

Add a geographical location

Add a distribution record to a taxon

Add a new specimen

Add a feeding type to a taxon

Add a link to a taxon

Add a note to a taxon

Add a image to a taxon

How to edit information in the database

Change a taxon name

Change the status of a name

Change the record status

Change (the status of) a distribution

Change (the identification of) a specimen

How to remove information from the database/website

Annex 1. Aphia special collections

Regional registers

ERMS - European Register of Marine Species

URMO – UNESCO-IOC Register of Marine Organisms

TISBE - Taxonomic Information System for the Belgian coastal area.

NSBP - North Sea Benthos Project

NWARMS - North West Atlantic Register of Marine Species

RAMS - The Register of Antarctic Marine Species

MASR - Marine Arctic Species Register

MARECO - pelagic biodiversity in the open ocean along the Mid-Atlantic Ridge

MASDEA - Marine Species Database for Eastern Africa

BlackSea - Black Sea species checklist

Macrobel - Macrobenthos of the Belgian Continental Shelf

Non-indigenous species in Belgium

Global thematic registers

HABs - IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae

Non-indigenous species

Global species registers

Platyhelminthes - World database of Proseriata and Kalyptorhynchia

Nemertina - Nemertina World Checklist

Porifera - World Porifera Database

Ostracoda - World check list of Halocyprida

Cumacea - World check list of Cumacea

Hydrozoa - World list of Hydrozoa

Amphipoda - World Amphipoda database

Brachiopoda - Brachiopoda world database

Phoronida - Phoronida world database

Crinoidea - World List of the Crinoids

Ophiuroidea - World Ophiuroidea Database

Euphausiacea - Euphausiacea World list

Isopoda - World List of Marine Freshwater and Terrestrial Isopod Crustaceans

Mangroves - World List of Mangroves

Pisces - World Database of Marine Pisces

Polychaeta - World Register of Polychaeta

Pycnogonida - Pycnogonida World Database

Ascidiacea - World list of Ascidiacea

NeMys

Annex 2. List of main tables and fields in the WoRMS database

Taxonomical information

Source information

Vernacular information

Distribution information

Specimen information

Feeding type information

Image information

Note information

Geographical information

The WoRMS database system

Background

It is the VLIZ database, called Aphia, initially a local initiative to store and disseminate species information of the Belgian part of the North Sea, that now serves as the IT platform for WoRMS. The main purpose of the development of the database was to support all the biological data management activities at VLIZ, and to make sure taxonomy used in the different projects was consistent.The users of this database aredata managers, taxonomists, ecologists, volunteer researchers and the general public.

The VLIZ data centre is internationally recognized in biological data management and on behalf of the European Network of Excellence MarBEF hosts the European Register of Marine Species (ERMS) and has developed and manages the European Node of the Ocean Biogeographic Information System (EurOBIS). VLIZ, with support from MarBEF and in close collaboration with OBIS has started the initiative to use the Aphia database and online system to create a World Register of Marine Species.

WoRMS receives also support from GBIF, Richard Lounsbery Foundation and the new EU Funded project PESI. But many more resources are spent indirectly to WoRMS through many efforts from individuals, projects and initiatives that contribute to WoRMS.

Through Aphia, 34 regional and global species databases are now brought together into a single information system.

Description of database

The MS SQL relational database structures can be found at:

Users

Web statistics

Month / Unique visitors / Number of visits / Pages / Hits / Bandwidth
Jan-07 / 2 / 3 / 517 / 768 / 3.35 MB
Feb-07 / 35 / 152 / 12101 / 14273 / 292.14 MB
Mar-07 / 115 / 514 / 26215 / 28223 / 764.35 MB
Apr-07 / 1254 / 1721 / 24955 / 35078 / 859.18 MB
May-07 / 3164 / 4425 / 54140 / 76843 / 1.18 GB
Jun-07 / 3191 / 4720 / 78135 / 103937 / 1.52 GB
Jul-07 / 3118 / 4700 / 66033 / 92365 / 1.72 GB
Aug-07 / 3084 / 5269 / 91110 / 128975 / 2.31 GB
Sep-07 / 3916 / 6862 / 124584 / 220206 / 4.12 GB
Oct-07 / 5698 / 9610 / 138760 / 207646 / 6.43 GB
Nov-07 / 6845 / 13439 / 156526 / 229469 / 23.07 GB
Dec-07 / 6799 / 12922 / 130270 / 209441 / 5.25 GB
Jan-08 / 6392 / 12294 / 183296 / 279687 / 9.76 GB
Feb-08 / 8054 / 14113 / 211842 / 321173 / 9.67 GB
Mar-08 / 10301 / 17536 / 309628 / 478981 / 16.42 GB
Apr-08 / 10947 / 19161 / 307531 / 445042 / 8.06 GB
May-08 / 11865 / 19166 / 210003 / 346554 / 6.44 GB

List of organisations and people who have received copies of ERMS and WoRMS (end-users)

Government agencies

  1. Italy (Ministry of Environment)
  2. Italy (Nature Protection Directorate)
  3. Germany (Federal Environmental Agency)
  4. Denmark (ICES)
  5. The Netherlands (RIKZ)
  6. France (EUNIS/European Topic Centre on Nature protection and Biodiversity)
  7. Belgium (MUMM)
  8. UK (JNCC)

Research organisations

  1. Greece (HCMR)
  2. France (IFREMER)
  3. France (MNHN)
  4. France (SB Roscoff)
  5. USA (National Cancer Institute)
  6. Italy (SZN)
  7. UK (MBA)
  8. Denmark (NERI)
  9. USA (MBL)
  10. Australia (CSIRO)
  11. Germany (IFM-GEOMAR)
  12. Germany (BGBM)
  13. Sweden (Hafok)

Universities (Researchers, Students)

  1. USA (UCSD)
  2. Germany (Freie Universität Berlin)
  3. France (USTL)
  4. Greece (University of Aegean)
  5. Denmark (University of Aarhus)
  6. Canada (University of British Columbia, Fisheries Centre)
  7. Spain (Universidade da Coruña)
  8. UK (UCL)

SMEs

  1. Norway (Akvaplan-niva)
  2. France (CREOCEAN)
  3. New Zealand (Saatchi & Saatchi)
  4. UK (Finding Sanctuary, Unicomarine Ltd.)

Data progress

Number of records:

  • Taxon names: 224,660
  • Valid species: 122,518
  • Synonyms: 56,391
  • Sources: 45,663
  • Distributions: 194,461
  • Specimens: 2,511
  • Pictures: 5,657
  • Notes: 84,634
  • Links: 27,315
  • Feeding types: 8,929
  • Taxonomic editors: 149

Special collections

So far 13 Regional species databases, two global thematic databases and 19 global species databases have been integrated into Aphia (table 1). Each database forms a special collection in Aphia and most of them have their own separate website (see annex 1 for a description of all the collections). The collections are formed on the basis of assigning a context to a record, being a name, a source, a distribution, a specimen etc..

In total, we integrated 311,234 taxon names of which 224,442 were species and 61,861 were species synonyms. After integration (eliminating identical entries), 224,654 (about 70% of the above number of taxon names) were retained.

160,733(+9,504 which are not part of a special collection), or 55% of all thetaxon names were unique, belong to no or only one collection.

Of the 286,303species names we received, 134,007 (+7,467 which are not part of a special collection) or 49% were unique, belong to no or only one collection.

Table 1. overview of the species databases that are integrated in Aphia together with the number of names, species and valid species names they represent.

all names / all species / valid species
Regional registers
ERMS - European Register of Marine Species / 54603 / 37611 / 31629
URMO - UNESCO-IOC Register of Marine Organisms / 24291 / 20505 / 19000
TISBE - Taxonomic Information System for the Belgian coastal area. / 21944 / 11280 / 8509
NSBP - North Sea Benthos Project / 3533 / 1599 / 1387
NSBS - North Sea Benthos Survey / 2028 / 847 / 770
NWARMS - North WestAtlantic Register of Marine Species / 12011 / 6122 / 5724
RAMS - The Register of Antarctic Marine Species / 13268 / 7649 / 7064
MASR - Marine Arctic Species Register / 3237 / 1347 / 1244
MARECO - pelagic biodiversity in the open ocean along the Mid-Atlantic Ridge / 41 / 13 / 10
MASDEA - Marine Species Database for Eastern Africa / 30098 / 20479 / 17680
BlackSea - Black Sea species checklist / 3210 / 1348 / 1238
Macrobel - Macrobenthos of the Belgian Continental Shelf / 1032 / 364 / 315
Non-indigenous species in Belgium / 547 / 63 / 63
Global thematic registers
HABs - IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae / 293 / 182 / 91
Non-indigenous species / 2075 / 713 / 675
Global species registers
Platyhelminthes - World database of Proseriata and Kalyptorhynchia / 1289 / 976 / 733
Nemertina - Nemertina World Checklist / 2928 / 2363 / 1348
Porifera - World Porifera Database / 18470 / 15531 / 8194
Ostracoda - World check list of Halocyprida / 325 / 244 / 244
Cumacea - World check list of Cumacea / 1453 / 1296 / 1287
Hydrozoa - World list of Hydrozoa / 2225 / 1559 / 1283
Amphipoda - World Amphipoda database / 3774 / 2819 / 2477
Brachiopoda - Brachiopoda world database / 633 / 411 / 404
Phoronida - Phoronida world database / 29 / 24 / 11
Crinoidea - World List of the Crinoids / 130 / 94 / 94
Ophiuroidea - World Ophiuroidea Database / 4345 / 3772 / 2153
Euphausiacea - Euphausiacea World list / 107 / 87 / 86
Isopoda - World List of Marine Freshwater and Terrestrial Isopod Crustaceans / 14763 / 12191 / 10063
Mangroves - World List of Mangroves / 198 / 121 / 72
Pisces - World Database of Marine Pisces / 52731 / 42359 / 16905
Polychaeta - World Register of Polychaeta / 20461 / 17007 / 11397
Pycnogonida - Pycnogonida World Database / 1430 / 1326 / 1310
Ascidiacea - World list of Ascidiacea / 5562 / 5188 / 2745
NeMys / 8170 / 6952 / 6376

Editing, rights and data quality

The Aphia database is build up from regional and global species databases and work that is done by the database management team. When the taxonomic experts provided us with a list of names, the database management team entered the data and logged in with the login details of the taxonomic expert. The database management team also entered names from sources such as publications and datasets, which means names that do not directly come from the taxonomic experts. In that case, they log in with their own login details.

A quality flag is attached to each taxon name, based on the status of the person who created or changed the record in the database.

The quality flag is indicated at two levels:

  • The record status, by stating who has added/edited the name (database management team or taxonomic expert and the name of the person is listed in the edit history)
  • Thestatus of the name:
  • When added/edited by database management team:
  • Accepted(in grey)
  • Unaccepted, and all other possibilities (in orange)
  • When added/edited by a taxonomic expert:
  • Accepted (in black)
  • Unaccepted, and all other possibilities (in red)

Only taxonomic experts and members of the database management team have access to add/edit information online. Access rights for taxonomic experts are based on the taxonomic hierarchy, which means they can only add/edit information to their specific taxon group.

A lot of information in Aphia has been entered by the database management team. For every record, the source of information is added (be it a publication, database or expert person). This means however, that a lot of the information has not been validated by the taxonomic experts. At this moment, all the information is shown on the WoRMS portal. However, only the information that is part of a collection, is shown on the collection websites (e.g. only the information that has the isopod context, is shown on the isopod portal,

In total, Aphia holds 224,653 taxon names, of these:

  • 104,464 are not checked by a taxonomic expert (75,273 if you exclude ERMS).
  • 161,629 are valid names, of which 90,099 are not checked by a taxonomic expert (63,287 if you exclude ERMS)

In total, Aphia holds 178,906species names, of these:

  • 77,076 are not checked by a taxonomic expert (54,464 if you exclude ERMS)
  • 122,515 are valid names, of which 65,140 are not checked by a taxonomic expert (44,646 if you exclude ERMS).

Table 2. gives an overview of the number and percentage of valid names (belonging to the taxon corresponding to each collection) that are in Aphia, but are not part of the global species databases. And the number of these names that are not validated by taxonomic experts, and the number of names that derive from ERMS.

All names in: / valid names not in: / % / non-checked / from ERMS
World database of Proseriata and Kalyptorhynchia / 1289 / 218 / 14 / 210 / 147
Nemertina World Checklist / 2928 / 7 / 0 / 6 / 0
World Porifera Database / 18470 / 106 / 1 / 93 / 0
Ostracoda - World check list of Halocyprida / 325 / 1112 / 77 / 1112 / 694
World check list of Cumacea / 1453 / 42 / 3 / 42 / 1
World list of Hydrozoa / 2225 / 2899 / 57 / 2899 / 0
World Amphipoda database / 3774 / 61 / 2 / 61 / 0
Brachiopoda world database / 633 / 0 / 0 / 0 / 0
Phoronida world database / 29 / 3 / 9 / 2 / 0
World List of the Crinoids / 130 / 303 / 70 / 200 / 62
World Ophiuroidea Database / 4345 / 70 / 2 / 69 / 4
Euphausiacea World list / 107 / 3 / 3 / 3 / 0
World List of isopods / 14763 / 209 / 1 / 119 / 46
World List of Mangroves / 198 / 0 / 0
World Database of Marine Pisces / 52731 / 463 / 1 / 463 / 68
World Register of Polychaeta / 20461 / 1048 / 5 / 819 / 320
Pycnogonida World Database / 1430 / 230 / 14 / 200 / 0
World list of Ascidiacea / 5562 / 267 / 5 / 238 / 3
NeMys / 8170 / 497 / 6 / 497 / 365

Future developments

List of planned new system developments:

  • Shopping basket to download lists of species names and additional information (specimens, references, distributions, notes, …) as spreadsheets in MS Excel, PDF, MS Access. Including selection of the quality status flags.
  • Facilitate off-line editing by providing spreadsheets for editing and re-importing.
  • Automated message to the Tax Editor when new information is added or existing information is changed by another member of the editorial board for a particular taxon.
  • Add expert-validated quality flags with other types of information
    (not only taxon names, e.g. distribution, specimen, feeding type, image, …). Organise queue for non-validated information.
  • Further develop the online ID key tool: improve layout, include tool to import/export files.
  • Browse distributions based on the gazetteer (include specimen distribution records) and add maps to distributions.
  • Add hierarchical habitat list (suggestions?).
  • New layout/webdesign, making synonyms and supplemental (non-expert validated) information less prominent. Search options: e.g. guide the visitor directly to the accepted name.
  • Set-up a mailing list for publishers to inform taxonomists/experts about newly published papers on a particular taxon.
  • Online editing manual (video screen capture).
  • Update fuzzy tool: new Tony Rees implementation
  • New check tools: double taxon checker, double gu checker.
  • Images: send reason for deletion to image provider, allow image uploads for specimens
  • Different taxonomic tree views: display valid names only, valid + synonyms, ...)
  • Add citation of each register, per special collection
  • Develop online delete archive + edit history (~Wiki)
  • Enable record locking, after validation by taxonomic expert
  • Create LSIDs
  • Implement data exchange formats (TAPIR?)
  • Other suggestions?

Future ideas

  • Enable Tax editors to create news items on the homepage, as a mechanism to advertise new species discoveries.

How to retrieve information from the database

Through the website

You can:

  • Search for a taxon (any rank)
  • Search for taxa described by a particular author
  • Search for taxa described in a particular year
  • Search for a taxon by ID (WoRMS ID/TSN ID)
  • Search for a taxon by common name
  • Search for a reference, and list species
  • Search for a geographic location, and list species
  • Search for a picture of a species
  • Search for a specimen

Select extra criteria: only valid names (on/off), only marine names (on/off)

Generate a list of taxa that corresponds to a number of criteria.

Some examples:

  1. Leave taxon field blank
  2. Select validity/marine, e.g. only valid names of marine species
  3. Select rank (equal to, lower or equal to, higher to), e.g. equal to species
  4. Select higher taxon group, e.g. Holothuriidae

creates list of all valid species names of Holothuriidae.

  1. Search for authority that contains a publication date = 2004
  2. Select only valid names of marine species
  3. Select rank equal to species
  4. Select Holothuriidae as higher taxon group

creates list of new holothuriid species published in 2004

  1. Search for a geographic location
  2. In/exclude subareas (is based on parent-child relationships of geographic locations in our marine gazetteer)
  3. Select rank
  4. Select higher taxon group
  5. Select validity of distribution record (Certainly valid; Also probably valid; Also probably false; All records)
  6. Select synonyms (Sort on synonyms, list valid names; Sort on valid names, list synonyms; Only valid names)

e.g. create a distinct list of fish species that are without mention of incorrectness observed in Belgian marine waters (and include all subareas).

  1. Search for a specimen
  2. Select by code
  3. Select by type (holo-, lecto-, neo-, syn-, topo-, para-, allo-, paralecto-, co-) /non-type/all types
  4. Select specific museum (drop down-list)/all locations
  5. Select taxon rank
  6. Limit to higher taxon

e.g. create a list of holotype specimens from the genus Actinopyga.

Extra search criteria for Taxonomic editors

  • Limit to non-checked (not expert validated) names
  • Limit to Marine/Brackish/Fresh/Terrestrial environment (Yes/No/Unknown)
  • Limit to a specific collection and/or exclude a specific collection

e.g. create a list of Porifera species names, not validated by a Tax expert, that are part of the European Register of Marine Species, and are not listed in the World Porifera Database.

Through the download page

Every month we freeze a monthly version of the database and make these monthly back-ups available from the download page (

You need a password to access this webpage. Tax editors can simple ask for this by email (). Non-taxonomic editors need to fill in the request form (downloadable from the home page).

The database is a simple version of the actual database and contains:

  1. All the taxonomic and related information
  2. WoRMSID
  3. Taxon name linked to parent taxon
  4. Sources
  5. Environment flags
  6. Notes
  7. Vernacular names
  8. Distribution records
  9. Collection context
  10. Taxon tree to browse the taxonomic hierarchy
  11. Export tool
  12. Select higher taxon
  13. Select rank, e.g. down to subspecies level
  14. Delimiter, e.g. tab, comma, …
  15. Select collection context, e.g. ERMS, …

E.g. creates excel sheet of all taxa of Isopoda belonging to the ERMS context

Through the taxon match tool

You can use the WoRMS Taxon Match Tool to automatically match your species list or taxon list with WoRMS. After matching, the tool will return your file with the WoRMS IDs, valid names (notifies when your name is an unaccepted synonym), authority and publication date, the hierarchical classification, qualitystatus (expert validated or not). When there are no exact matches the system provides a pick-list of all possible matches.

For performance reasons, the limit is set to 1,000 rows. You can send larger files to and we will return the results to you as soon as possible.

Through the webservice

As a user or developer you can use the WoRMS webservice to feed your own application with standard WoRMS taxonomy. We currently support the platform-independent SOAP/WSDL standard. A few example of possible applications:

  • get the AphiaID for your taxon
  • check the spelling of your taxa
  • get the authority for your taxa
  • get the full classification for your taxa
  • resolve all your invalid names to valid ones
  • match your species list
  • resolve a common name to a scientific name