May 2009 - tdwg - lists.tdwg.org

e-Biosphere
by Lee Belbin 25 May '09

25 May '09

Dear Members and Friends As many of you would know, TDWG has a booth at e-Biosphere next week and I'll be manning (personning?) it. If you are going to be at the meeting and could give me a 15 minute break on the booth for a coffee etc, please let me know or just swing by. Look forward to seeing some of you. Lee Lee Belbin TDWG Secretariat

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Call for participation in GEO BON work groups
by Eamonn O Tuama (GBIF) 12 May '09

12 May '09

[apologies for cross posting] The establishment of the Group on Earth Observations Biodiversity Observation Network (GEO BON) was approved by GEO members at the GEO V Plenary in Bucharest last November (http://www.gbif.org/Stories/geobon). This is a culmination of efforts by many organisations, including GBIF, who have devoted time to developing both a concept document and implementation overview document for GEO BON. As a worldwide initiative, GEO BON, a component of the Global Earth Observation System of Systems (GEOSS) seeks to link and build on the work of countries, organisations and individuals to collect, manage, share and analyse data on the status of the world's biodiversity. For further information, visit the GEO BON home page: http://www.earthobservations.org/cop_bi_geobon.shtml GEO BON is now entering its implementation phase, and to aid this, a number of topical working groups are being established. Work Group 8 "Data Integration and Inter-operability; Informatics and Portals" is being lead by GBIF through co-chairs Hannu Saarenmaa (GBIF Finland) and Éamonn Ó Tuama (GBIF Secretariat). The attached document describes how the working groups should get started. If you are interested in participating in a work group, please contact the chair of the group as listed in the document. In particular, for work group 8 (Data Integration and Interoperability), please contact the co-chairs below by Friday, 5th June. Best regards, Hannu and Éamonn Hannu Saarenmaa GBIF Finland hannu.saarenmaa(a)helsinki.fi Telephone +358-9-191-28688 Mobile +358-50-3102689 http://www.gbif.fi/ Éamonn Ó Tuama GBIF Secretariat eotuama(a)gbif.org Telephone +45 3532 1494 http://www.gbif.org

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Re: [tdwg] Ideas on having Harvesters like GBIF clean, flag inconsistencies, and add additional value to the data
by Donald.Hobern＠csiro.au 12 May '09

12 May '09

Thanks, Peter. In fact GBIF is already doing much of what you describe, and the ALA (and I am sure several other projects) are planning to go further in the same direction. The GBIF data portal already flags records with apparent coordinate issues and with apparent mismatches between coordinates and stated country, as well as flagging records with scientific names with impossible formats, records without a clear indication of the basis of record, impossible dates, etc. I believe that this information is accessible as part of the responses from the web service. The ALA has been building on the ALA portal software (in particular to index records against smaller administrative units within Australia). We are also planning to identify records which are potentially sensitive (species endangered or considered a biosecurity threat nationally or in the region where it was recorded) and to report these to data providers. My current thinking is that we should offer this as a service which can both be executed during harvesting and also as a stand-alone service for which users can submit a batch of Darwin Core-style records (probably tab-delimited) and get back a report for whichever set of tests or value-add operations they choose. This could help providers with data cleaning even before they share their data (and also could help them to make sure there are no known sensitivity issues around their data). Such a service could be extended more or less indefinitely to report more and more aspects of interest. One of the major options could be to cross-reference records to accepted taxonomic authorities (via LSIDs or other identifiers). Best wishes, Donald Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au Web: http://www.ala.org.au/ -----Original Message----- Date: Fri, 8 May 2009 19:23:32 -0500 From: Peter DeVries <pete.devries(a)gmail.com> Subject: [tdwg] Ideas on having Harvesters like GBIF clean, flag inconsistencies, and add additional value to the data To: tdwg(a)lists.tdwg.org Message-ID: <3833bf630905081723l2f1d5369je8af6b0e4a26324d(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Arthur Chapman sent me some good comments regarding Datums etc. The discussion made me realize that there may be a need for two types of formats. One for the providers and a second one that is output by the harvesting service. This is because the needs and abilities of the data providers are different than the needs and abilities of those who would like to consume the data. Consumers, who analyze and map the data, would like something that is easy to process, standardized and as as error free as as possible. It could work in the following way. Data harvesters, like GBIF, collect the records. Run them through cleaning algorithms that check attributes including that the lat and long actually match the location described. These harvesters would then expose this cleaned data via XML and RDF with tags that flag possible inconsistencies. The harvesters would also add a field for the lat and long in WGS84 if the original record contains a valid Datum. Those records without a Datum would still be exposed but the added geo:latitude and geo:longitude fields would be empty. I can imagine that that data uploaded to GBIF and other harvester services will be replete with typo's and inconsistencies that will frustrate people trying to analyze or simply map the data, the harvester services could add value by minimizing these frustrations. Originally, it seemed that a global service should standardize on a global Datum like WGS84. After all, we have standardized on meters? However, after discussing this with Arthur, I realize that this is not possible for a number of reasons. That said, I think the data would be much more valuable and less likely to be misinterpreted if if a version of it was available in WGS84. This solution would eventually encourage data providers to understand what a Datum is and include it in their data. It would also help solve a number of other data integration problems. Respectfully, Pete

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FW: [Taxacom] Biodiversity Informatics Survey for VertNet, Participation Requested
by Lee Belbin 10 May '09

10 May '09

And another survey... Lee Belbin TDWG Secretariat -----Original Message----- From: taxacom-bounces(a)mailman.nhm.ku.edu [mailto:taxacom-bounces@mailman.nhm.ku.edu] On Behalf Of Heather Constable Sent: Saturday, 9 May 2009 10:29 AM To: taxacom(a)mailman.nhm.ku.edu Subject: [Taxacom] Biodiversity Informatics Survey for VertNet, Participation Requested Hello, Your feedback can help guide biodiversity informatics development. We are conducting a survey on potential tools and data sets to incorporate into the search portals of the MaNIS <http://manisnet.org/>, HerpNET<http://www.herpnet.org/>, ORNIS <http://olla.berkeley.edu/ornisnet/> and FishNet II<http://www.fishnet2.net/index.html>distributed database networks for natural history collections. Specifically, we would like to build tools that benefit users and publishers of biodiversity data. Your feedback is greatly appreciated. Please take a few minutes to complete this survey: http://www.questionpro.com/akira/TakeSurvey?id=1229513 Here <http://68.111.46.217/pres/PresentationServlet?action=home> is a demo portal serving MaNIS, HerpNET, ORNIS and FishNet II data through into a single VertNet search portal, in its current form. The survey does not specifically critique the functions of the this portals, but it may help to imagine the exciting potential for mapping, visualization and validation tools. Results will be posted on the VertNet website: http://vertnet.org<http://vertnet.org/index.php>/ VertNet is a collaboration between the National Biological Infrastructure ( NBII <http://www.nbii.gov/portal/server.pt>), the Museum of Vertebrate Zoology at the University of California, Berkeley (MVZ<http://mvz.berkeley.edu/>), University of Kansas Natural History Museum and Biodiversity Research Center (KUNHM <http://www.nhm.ku.edu/>), Tulane University Museum of Natural History (TU <http://www.museum.tulane.edu/>), Harvard University Museum of Comparative Zoology (MCZ <http://www.mcz.harvard.edu/>), University of Colorado Museum (UCM) <http://cumuseum.colorado.edu/>, Field Museum (FMNH<http://www.fieldmuseum.org/>) and the American Museum of Natural History (AMNH <http://www.amnh.org/>) with over 100 other participating institutions. Apologies for cross postings. -- Heather Constable VertNet Coordinator Museum of Vertebrate Zoology University of California, Berkeley 3101 Valley Life Sciences Building 3160 Berkeley, California 94720 (510) 643-1620 http://vertnet.org/ _______________________________________________ Taxacom Mailing List Taxacom(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/taxacom The Taxacom archive going back to 1992 may be searched with either of these methods: (1) http://taxacom.markmail.org Or (2) a Google search specified as: site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here

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FW: [Taxacom] GBIF Content Needs Assessment Survey launched
by Lee Belbin 10 May '09

10 May '09

Apologies for the cross-posts but.... Lee Belbin TDWG Secretariat -----Original Message----- From: taxacom-bounces(a)mailman.nhm.ku.edu [mailto:taxacom-bounces@mailman.nhm.ku.edu] On Behalf Of Vishwas Chavan (GBIF) Sent: Friday, 8 May 2009 8:15 AM To: taxacom(a)mailman.nhm.ku.edu Subject: [Taxacom] GBIF Content Needs Assessment Survey launched GBIF CONTENT NEEDS ASSESSMENT SURVEY LAUNCHED The GBIF Secretariat is pleased to announce the launch of the 'Content Needs Assessment Survey' prepared by the GBIF Content Needs Assessment Task Group. The Survey in English, Spanish and French will be open for respondents until 12th June 2009. Please click on the link below to see details of the survey announcement in English, Spanish and French. http://www.gbif.org/News/NEWS1241701184 Link to Survey: English version: http://www.surveymonkey.com/s.aspx?sm=XWXP0hKQSbFwb4fgn5uZ_2bQ_3d_3d Spanish version: http://www.surveymonkey.com/s.aspx?sm=0if6UAmPkGpjVb_2felOHV0w_3d_3d French version: http://www.surveymonkey.com/s.aspx?sm=qCDkmXzlQJYB5Ph5m2vk4w_3d_3d Through this announcement we request stakeholders and users of primary biodiversity data to participate in the Survey. We further request scientific institutions, multi-lateral organisations, national, regional and global funding agencies, academicians, and citizen scientists to participate in the Survey. Please forward this announcement to all potential respondents. -- Vishwas Chavan, Ph.D. Senior Program Officer for DIGIT Global Biodiversity Information Facility 15 Universitetsparken, DK 2100, Copenhagen, Denamrk Tel. +45 35 32 14 75, Fax. +45 35 32 14 80 Email - vchavan(a)gbif.org Web - www.gbif.org _______________________________________________ Taxacom Mailing List Taxacom(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/taxacom The Taxacom archive going back to 1992 may be searched with either of these methods: (1) http://taxacom.markmail.org Or (2) a Google search specified as: site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here

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Wikipedia entries
by Lee Belbin 10 May '09

10 May '09

Dear TDWG Members and Friends There are two current issues that you may be able to help us with. One of our members noted that the Wikipedia entry for Darwin Core was out of date and possibly about to be deleted. Markus Döring subsequently added an excellent update for DwC. Thanks Markus! I then thought that it would be really helpful for our community to have similar useful entries for ABCD, NCD, SDD (BD), TAPIR, TCS...? Donald has also raised the need for a better introduction to Biodiversity Informatics, and there are other topics that would be good to see an entry for. I've just done a minor update on my original TDWG entry but more input would be good to see. This relates to the second issue. We have had a request from a biology historian about a history of TDWG. A few of us are unaware of anything written specifically about TDWG's history, but do have links to various past meetings at http://www.tdwg.org/about-tdwg/past-meetings/, but we are missing 1987-1997. I've put the request through to Frank Bisby, Jim Croft, Adrian Rissone and Stan Blum. Frank and Jim have some paper material that may be able to be scanned, but if anyone is aware of anything that may be useful for this, please let me know. From what I can tell, an uncensored of TDWG would make a nice read. J Thanks Lee Lee Belbin TDWG Secretariat

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Ideas on having Harvesters like GBIF clean, flag inconsistencies, and add additional value to the data
by Peter DeVries 08 May '09

08 May '09

Arthur Chapman sent me some good comments regarding Datums etc. The discussion made me realize that there may be a need for two types of formats. One for the providers and a second one that is output by the harvesting service. This is because the needs and abilities of the data providers are different than the needs and abilities of those who would like to consume the data. Consumers, who analyze and map the data, would like something that is easy to process, standardized and as as error free as as possible. It could work in the following way. Data harvesters, like GBIF, collect the records. Run them through cleaning algorithms that check attributes including that the lat and long actually match the location described. These harvesters would then expose this cleaned data via XML and RDF with tags that flag possible inconsistencies. The harvesters would also add a field for the lat and long in WGS84 if the original record contains a valid Datum. Those records without a Datum would still be exposed but the added geo:latitude and geo:longitude fields would be empty. I can imagine that that data uploaded to GBIF and other harvester services will be replete with typo's and inconsistencies that will frustrate people trying to analyze or simply map the data, the harvester services could add value by minimizing these frustrations. Originally, it seemed that a global service should standardize on a global Datum like WGS84. After all, we have standardized on meters? However, after discussing this with Arthur, I realize that this is not possible for a number of reasons. That said, I think the data would be much more valuable and less likely to be misinterpreted if if a version of it was available in WGS84. This solution would eventually encourage data providers to understand what a Datum is and include it in their data. It would also help solve a number of other data integration problems. Respectfully, Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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Test Example of Occurrence RDF with DarwinCore/TDWG (might not be correct :-\)
by Peter DeVries 08 May '09

08 May '09

I thought I would try to start using the DarwinCore vocabulary in my observation RDF. I thought it might be easiest to start with the SimpleDarwinCore. The following URL takes you to an RDF file that combines my older vocabulary with my attempt at the SimpleDarwinCore. There is some redundancy in this version but it looks like I can probably replace a number of my terms with DarwinCore terms. The DarwinCore representation appears at the bottom of the RDF. http://species.geospecies.org/observations/a3c39dad-6756-4129-9a61-fbd32883… I would appreciate comments or suggestions. Thanks! Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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Test Example of Occurrence RDF with DarwinCore/TDWG (might not be correct :-\)
by Peter DeVries 08 May '09

08 May '09

I thought I would try to start using the DarwinCore vocabulary in my observation RDF. I thought it might be easiest to start with the SimpleDarwinCore. The following URL takes you to an RDF file that combines my older vocabulary with my attempt at the SimpleDarwinCore. There is some redundancy in this version but it looks like I can probably replace a number of my terms with DarwinCore terms. The DarwinCore representation appears at the bottom of the RDF. http://species.geospecies.org/observations/a3c39dad-6756-4129-9a61-fbd32883… I would appreciate comments or suggestions. Thanks! Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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