world register of marine species and aphia it platform
DESCRIPTION
World Register of Marine Species and Aphia IT platform. Ward Appeltans [email protected]. Introduction to WoRMS Framework What (data & statistics) Who (editorial board, SC and data managers) Aphia IT platform (How) online edit interface - PowerPoint PPT PresentationTRANSCRIPT
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FADA workshop, 5-7 December 2008 in Bruges (Belgium)
World Register of Marine Speciesand Aphia IT platform
Ward [email protected]
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FADA workshop, 5-7 December 2008 in Bruges (Belgium)
overview
• Introduction to WoRMS– Framework– What (data & statistics)– Who (editorial board, SC and data managers)
• Aphia IT platform (How)– online edit interface– Publication (website, citations, database download)– Tools (taxon match, webservice)
• Future plans
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History
• In 1999, VLIZ developed Aphia, a taxonomic database to support local researchers, and which resulted in a species register for the Belgian part of the North Sea.
• In 2004, VLIZ hosts the European Register of Marine Species and sets up the European Node of OBIS , with funding from MarBEF (EU FP7)
• From 2004 onwards, more registers came to VLIZ and more grew from Aphia, via the online edit interface (e.g. RAMS)=>World Register of Marine Species
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www.marinespecies.org
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www.marbef.org/data/erms.php
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www.marinespecies.org/copepoda
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www.marinespecies.org/hab
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www.scarmarbin.be/rams.php
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FADA workshop, 5-7 December 2008 in Bruges (Belgium)
What data?
• Minimal– Classification, Species name, Authority and
publication date• Highly desired
– Basionym, Original publication reference, Holotype information (type locality, museum, number, ..)
• Optional– additional synonyms, references, images,
morphological description, specimens, distribution, feeding type, host, weblinks, PDFs
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StatisticsTaxon names 236023Valid species 128752Synonyms 59751Sources 123171Distributions 195645Specimens 2911Pictures 7558Notes 85911Links 29730Feeding types 10524
(+ ~12,000 non-marine names; 5%)
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Data quality
The amount of data is increasing. In 2008:
74,000 names were added; 26,000 names were updated.
– 30% of all taxon names is not validated as yet (this was 40% in June 2008)
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Taxonomic editors in – Aphia: 176– WoRMS: 87– ERMS: 72– RAMS: 58– FADA: 58
• ERMS & WoRMS: 32• RAMS & WoRMS: 12• ERMS & RAMS: 11• Aphia & FADA: 10
• WoRMS, ERMS and FaEu united in SMEBD
Taxonomic editors
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www.smebd.eu
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Steering Committee &Data Managers
• 10 SC members (1 chair)– Yearly election
• Data managers (one ex-officio SC member)• IT developer
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Expert info and access control
Security Tools dbAphia db IMIS db
Contact detailsPeople Insitutions
LiteratureDatasetsProjects..
Login detailsUsernamePassword
IMIS IDAccess context
e.g. Aphia, VLIMAR, photogallery, news, MDA, ..
Aphia Editor detailsName and login information
Aphia taxon IDAphia collection
e.g. WoRMS, ERMS, RAMS, ..
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Aphia platform
• Hard & software:
– MS SQL– PHP out/input webinterface– MS Access front end
• manage editors, quality control (e.g. find duplicates)
– Apache running on Windows server– back-up (daily)
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Online Edit interface
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Data quality
• Data are entered/edited by– Taxonomic experts (TE)– Other experts– Data managers (based on
publications/datasets, or on behalf of TE)• Quality flags for:
– Record status• Checked by TE or added by DMT
• Public/non-public flags
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Citations
When verified by expert/contributed by GSD• Editors (Year). Taxon + Authority. In: GSD title.
Accessed through the World Register of Marine Species at URL on [date].
[author(s)] [Year]. [chapter] in [Book]. [Publisher]. [Page]
When not verified=> WoRMS is author
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MS Access download
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1. All the taxonomic and related information – WoRMS ID – Taxon name linked to parent taxon – Sources – Environment flags – Notes – Vernacular names – Distribution records – Collection context
2. Taxon tree to browse the taxonomic hierarchy
E.g. export excel sheet of all taxa of Isopoda belonging to the ERMS context
MS Access download
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websiteFind information on
– a taxon (any rank) – taxa described by a particular author – taxa described in a particular year – a taxon by ID (WoRMS ID/TSN ID) – a taxon by common name – a reference, and list species – a geographic location, and list species – a picture of a species – a specimen
– Select extra criteria: only valid names (on/off), only marine names (on/off)
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website
• 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
– List latest additions/edits by a person after a certain date
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RSS feeds
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taxon match tool
Validate your species list against WoRMS and get standard WoRMS taxonomy back.
After matching, the tool will return your file with:– WoRMS IDs, valid names (notifies when your name is an
unaccepted synonym), authority and publication date, the hierarchical classification, quality status (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. • Already 1,000 files uploaded in 2008
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Retrieve data
• Through the taxon match tool
Taxon match - STEP 3Do the match and check for ambigous names
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WebserviceAs a user or developer you can use this service to feed your own application with standard taxonomy. We currently use the platform-independent SOAP/WSDL standard.
SOAP (Simple Object Access Protocol) is a way for a program running in one kind of operating system (such as Windows 2000) to communicate with a progam in the same or another kind of an operating system (such as Linux) by using the World Wide Web's Hypertext Transfer Protocol (HTTP) and its Extensible Markup Language (XML) defined by the Web Service Definition Language (WSDL), as a mechanisms for information exchange
A few examples of possible applications: – get the ID 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– get the sources/references for a taxon
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SOAP/WDSL web service
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Future plans
• Some developments
– Further develop the online ID key tool
– Online editing manual (video screen capture).