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Biodiversity Informatics Course open to Nordic graduate students, postdocs, and researchers
by Deb Paul 05 Jun '14

05 Jun '14

Hi Everyone, Thought you'd all like to know about this upcoming Biodiversity Informatics course, offered to Nordic graduate students, postdocs, and researchers. Kilpisjärvi calling: Order and Sense to Your Data at the Polar Frontier ForBio: proudly presents the first-time-ever course on biodiversity informatics and data management *More info:* http://www.forbio.uio.no/events/courses/2014/biodiv_informatics.html *When:* 29 July -1 August 2014 *Where:* Kilpisjärvi Biological Station, University of Helsinki, Finland http://www.helsinki.fi/kilpis/english/ *What:* A course for Nordic graduate students, postdocs, and researchers which explores data tools beyond MS Excel and R! What are the modern, efficient, mistake-proof ways to collect and manage field and lab data, identifiers, traits, and environmental variables? How can you store your data to easily integrate with external databases? This course covers basics of data collecting and data management but leaves out data analysis to other courses. *How much:* No course fee. Danish, Swedish, Norwegian, or Finnish PhD students and postdocs are encouraged to join ForBio - the Research School in Biosystematics, since members are reimbursed for course-related travel costs and accommodation in shared rooms and food at Kilpisjärvi Station. ForBio may also support masters students registered at Danish, Swedish, Norwegian, or Finnish universities who provide compelling evidence that they need the course for their thesis work. ForBio will not cover any expenses (e.g., food, travel, or accommodation costs) for other participants who have to be registered as ForBio associates to attend the course. Please pass along to any who might be interested in taking the course -- or developing a similar one. Best, Deb -- Upcoming iDigBio Events https://www.idigbio.org/calendar --Deborah Paul iDigBio Technology Specialist Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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delimiter characters for concatenated IDs
by "Dröge, Gabriele" 06 May '14

06 May '14

Hi everyone, I guess there might have been some discussions about proper delimiter characters in the past that I have missed. In several projects, first of all in GGBN (Global Genome Biodiversity Network, http://www.ggbn.org) there is a need for making a decision now. We need to reference between different records and databases and within Darwin Core we want to use the relatedResourceID to do so. During our GGBN workshop at TDWG last year we agreed on concatenating the traditional triple ID (Catalogue Number, Collection Code, Institution Code) and add further parameters if required too (e.g. GUID, access point). We have checked those parameters and can definitely not use a single character as delimiter. So my question to you is, if there are already some suggestions on using two characters together as delimiters. It would be great if we could find a solution more than one community could agree on. Otherwise I would like to open the discussion and suggest "\\", "||", "\|", "§|", "§§", or "\§". Best wishes, Gabi ----------------------------------------------------------------- Gabriele Droege Coordinator - DNA Bank Network Global Genome Biodiversity Network (GGBN) Berlin-Dahlem DNA Bank Women's Officer ZE BGBM Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin Koenigin-Luise-Str. 6-8 14195 Berlin Germany +49 30 838 50 139 www.dnabank-network.org<http://www.dnabank-network.org> www.ggbn.org<http://www.ggbn.org> www.bgbm.org<http://www.bgbm.org>

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Re: [tdwg-content] delimiter characters for concatenated IDs
by "Dröge, Gabriele" 06 May '14

06 May '14

Thanks Gregor! I must say I really like this idea for our short term solution! Will discuss this with my team. Best, Gabi Von: Gregor Hagedorn [mailto:gregor.hagedorn@mfn-berlin.de] Gesendet: Dienstag, 6. Mai 2014 13:57 An: Dröge, Gabriele Cc: tdwg-content(a)lists.tdwg.org Betreff: Re: [tdwg-content] delimiter characters for concatenated IDs On the original question: my preference when creating an identifier for the triplet would be to be transparent, and create the identifer with the dwc terms embedded, i.e. use institutionCode=BGBM&collectionCode=xxx&catalogNumber=289742874239872 as the "self-coined" identifier string. While "&" may not be unique, the delimiter &collectionCode= is very likely so. And it is transparent, self-documenting what is going on (and I do not mean that people need to parse it - which they could in either case) Gregor On 5 May 2014 15:24, "Dröge, Gabriele" <g.droege(a)bgbm.org<mailto:g.droege@bgbm.org>> wrote: Hi everyone, I guess there might have been some discussions about proper delimiter characters in the past that I have missed. In several projects, first of all in GGBN (Global Genome Biodiversity Network, http://www.ggbn.org) there is a need for making a decision now. We need to reference between different records and databases and within Darwin Core we want to use the relatedResourceID to do so. During our GGBN workshop at TDWG last year we agreed on concatenating the traditional triple ID (Catalogue Number, Collection Code, Institution Code) and add further parameters if required too (e.g. GUID, access point). We have checked those parameters and can definitely not use a single character as delimiter. So my question to you is, if there are already some suggestions on using two characters together as delimiters. It would be great if we could find a solution more than one community could agree on. Otherwise I would like to open the discussion and suggest "\\", "||", "\|", "§|", "§§", or "\§". Best wishes, Gabi ----------------------------------------------------------------- Gabriele Droege Coordinator - DNA Bank Network Global Genome Biodiversity Network (GGBN) Berlin-Dahlem DNA Bank Women's Officer ZE BGBM Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin Koenigin-Luise-Str. 6-8 14195 Berlin Germany +49 30 838 50 139<tel:%2B49%2030%20838%2050%20139> www.dnabank-network.org<http://www.dnabank-network.org> www.ggbn.org<http://www.ggbn.org> www.bgbm.org<http://www.bgbm.org> _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org<mailto:tdwg-content@lists.tdwg.org> http://lists.tdwg.org/mailman/listinfo/tdwg-content -- --------------------------- Dr. Gregor Hagedorn Head of Digital World and Information Science Museum für Naturkunde Berlin Leibniz-Institut für Evolutions- und Biodiversitätsforschung Invalidenstrasse 43, 10115 Berlin +49 (0)30 2093 8576 (work) +49-(0)30-831 5785 (private) gregor.hagedorn(a)mfn-berlin.de<mailto:gregor.hagedorn@mfn-berlin.de> http://www.naturkundemuseum-berlin.de http://linkedin.com/in/gregorhagedorn This communication, together with any attachments, is intended only for the person(s) to whom it is addressed. Redistributing or publishing it without permission may be a violation of copyright or privacy rights.

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synonyms in DwC Archives
by Hilmar Lapp 19 Mar '14

19 Mar '14

I'm looking for recommendations on how best to put synonyms for taxon records into DwC Archive format. I'm assuming that these would go into an extension file. Do I have this right? What I'm having more trouble with is determining the right column term. there's dwc:vernacularName, which is also in the examples, but what about synonyms of different types that come with taxonomies (such as NCBI's) or that result from merging taxonomies. There isn't an obvious candidate in DwC, and the list at http://rs.gbif.org/core/dwc_taxon.xmldoesn't have a suggestion either that would seem pertinent. Any suggestions, pointers to documentation or examples? -hilmar -- Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io

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why is relationshipOfResource defined as the inverse of what one would expect?
by Hilmar Lapp 19 Mar '14

19 Mar '14

Among the ResourceRelationship terms in DwC, we have the following key properties denoting subject and object of the asserted relationship: resourceID - "An identifier for the resource that is the subject of the relationship." relatedResourceID - "An identifier for a related resource (the object, rather than the subject of the relationship)." Then there is relationshipOfResource, which oddly and confusingly is defined as the inverse of a property relating subject to object: "The relationship of the resource identified by relatedResourceID to the subject (optionally identified by the resourceID)." The comment gives examples that do nothing to suggest that the definition has this backwards, or to disambiguate: "Examples: "duplicate of", "mother of", "endoparasite of", "host to", "sibling of", "valid synonym of", "located within"." The corresponding wiki page does not offer further clarification: https://code.google.com/p/darwincore/wiki/ResourceRelationship There is also a page on the TDWG-RDF wiki (which declares itself as obsolete, yet links to itself for further information): https://code.google.com/p/tdwg-rdf/wiki/ResourceRelationship The example on this page (Table 1) seems to assume (or is fooled or confused into thinking) that relationshipOfResource is not relating object to subject, but as one would expect subject to object. So is the definition wrong? And if it's not, why was the relationship chosen to point in the inverse direction of what one would expect? -hilmar -- Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io

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Usage of elevation, depth & distanceAboveSurface
by Markus Döring 15 Feb '14

15 Feb '14

Hi all, I am notoriously confused how to use the dwc terms that define the vertical position of a location. For each of elevation, depth and distanceAboveSurface there is a minimum and maximum term defined. Taking min/max aside, how do those 3 terms play together? From my common understanding elevation refers to the vertical position of the location relative to a reference point, usually the sea level. With negative values for places below the sea. Wikipedia seems to follow the same definition: http://en.wikipedia.org/wiki/Elevation The Darwin Core definition is a bit lose, but close: "The lower limit of the range of elevation (altitude, usually above sea level), in meters." The use of depth in that view is then only to give an idea how far below the (water) surface the location is (think pressure) - especially for places not in the sea like lakes. In the case of locations under the sea depth should then always be the negated value of elevation, is that true? I can see the use of the third term distanceAboveSurface from the drilling core in the only example given, but that is rather exotic. Would it not replace the term depth as a more generic version unrelated to water, for example to refer to locations up in trees? Would a use of the terms like this be correct? (A) a fish found 800m below the sea: dwc:minElevationInMeters = -800 dwc:minDepthInMeters = 800 dwc:minDistanceAboveSurfaceInMeters = -800 (B) a frog found on a tree, 20m above the ground which grows in 760m above the sea (measured from the ground): dwc:minElevationInMeters = 780 dwc:minDepthInMeters = dwc:minDistanceAboveSurfaceInMeters = 20 When reading the definition for minimumDistanceAboveSurfaceInMeters I doubt my understanding is correct and instead elevation is used as the primary reference point on top of which depth and then distanceAboveSurface is added: "The lesser distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation." It would be good to have that documented a bit more explicitly. Any advice appreciated. best, Markus

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dwc:genus & the canonical name
by Markus Döring 14 Feb '14

14 Feb '14

Hi all, we are currently improving our webservices at GBIF and do hit again the issue about whether dwc:genus represents the genus of the accepted or actually applied scientificName. So far GBIF has used the DWC definition and used dwc:genus as the genus the name had been classified into, i.e. the genus of the accepted name in case of synonyms. We would like to continue with that definition, but there had been requests to also expose the actual parsed name and would like to adopt the previously proposed but never ratified terms dwc:genericName and dwc:infragenericEpithet for this. See http://lists.tdwg.org/pipermail/tdwg-content/2012-March/002882.html for a quick summary of the previous discussions and the issue itself at google code: https://code.google.com/p/darwincore/issues/detail?id=151. As a backup to the proposal, i4Life / Catalogue of Life are also already using the newly proposed terms in their dwca format. Can we get an agreement to add those 2 terms to Darwin Core? best, Markus PS: It might be a good oppertunity to also add dwc:strain and dwc:cultivarEpithet https://code.google.com/p/darwincore/issues/detail?id=144 https://code.google.com/p/darwincore/issues/detail?id=141

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Apply now: Hackathon at the Netherlands Natural History Museum
by Rutger Vos 10 Feb '14

10 Feb '14

Dear colleagues, Recent years have seen a surge in projects that produce large volumes of biodiversity data. Examples of these are structured, machine-readable data as extracted from digitised heritage biodiversity literature, species occurrence data, comparative data for phylogenetics, taxonomies, digitised collection specimens, and so on. These data can be represented in a variety of standards-compliant interchange formats (using XML, RDF, JSON, etc.) making them amenable to processing by generic, open source "data enrichment" workflows. The idea is simple - enrich biodiversity data with meaningful links to related resources, such as links from named locations to standardized georeferences, links from taxon names to taxon concept URIs, links from characters and traits to trait ontologies, links to relevant images, semantic descriptions of data provenance, links to publications, and so on. To this end, we would like to invite you to the "Data enrichment hackathon" that will take place March 17th - 21st, 2014 at the Naturalis Biodiversity Center, in Leiden, the Netherlands. The hackathon will bring together domain experts in biodiversity informatics from a variety of subdisciplines to be creative with biodiversity data and to write code. The end result will be open source tooling that will allow stakeholders to re-use and enhance biodiversity knowledge. We think that such tooling might include tools that add properties to data; that convert between formats, expanded controlled vocabularies or ontologies; data integrators; annotations and query tools, etc. The hackathon is organised with the support of Naturalis [1] in the scope of the pro-iBiosphere project[2], an FP7 e-infrastructure project that focuses on making biodiversity data and information (now entrapped in literature) open, linked and digital. pro-iBiosphere has the vision of implementing an Open Biodiversity Knowledge Management System (OBKMS), i.e. an integration platform that will allow to produce Biotas (i.e. Floras, Faunas, Mycotas and other revisionary taxonomic literature) of the future in a flexible semantically-driven online environment. We would very much appreciate if you can state your intent to participate by the 14th of February 2014 at the latest. In order to facilitate the organisation of the event and be aware of your interests and specialties please fill in a brief questionnaire [3]. We have limited funding to support the participation and travel costs of a number of participants. In case you need funding to join the Hackathon, please indicate this in your response to the questionnaire. If you are not able to participate but have suggestions for other colleagues that could join the hackathon, please let us know. The agenda, accommodation and other relevant information is available on our wiki[4]. For any additional question please email Rutger.Vos(a)naturalis.nl or Soraya.Sierra(a)naturalis.nl. We look forward to seeing you in Leiden! With best regards, Rutger Vos and Soraya Sierra [1] http://www.naturalis.nl [2] http://www.pro-ibiosphere.eu/[3] http://tinyurl.com/NBCDataHackForm [4] http://wiki.pro-ibiosphere.eu/wiki/Data_enrichment_hackathon,_March_17-21_2…

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Fwd: Environmentally related information
by Annett P 14 Jan '14

14 Jan '14

---------- Forwarded message ---------- From: <tdwg-content-owner(a)lists.tdwg.org> Date: 15 Jan 2014 07:56 Subject: Environmentally related information To: <ap16709(a)gmail.com> Cc: You need to be subscribed to this mailing list in order to post messages ---------- Weitergeleitete Nachricht ---------- From: Annett P <ap16709(a)gmail.com> To: tdwg-content(a)lists.tdwg.org Cc: Date: Tue, 14 Jan 2014 19:56:40 +0100 Subject: Environmentally related information I was wondering whether it has been attempted/it is feasible to use the standards of observations and measurements ( http://www.opengeospatial.org/standards/om) to describe sampling procedure and environmental context of a species instead of extending DwC with terms? Any hint is very much appreciated. Best regards Annett

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New Term Request - typifiedName
by John Wieczorek 14 Jan '14

14 Jan '14

Dear all, This message is to open public commentary on a request for a new term, typifiedName, submitted by Markus Döring to the Darwin Core issue tracker at https://code.google.com/p/darwincore/issues/detail?id=197. The justification given for inclusion of the term is: "Clear separation of the type status and the typified scientific name that is typified by a type specimen, the subject. Looking at how dwc:typeStatus has been used in all of GBIFs specimen data one can see there is the need to express this, but it should better be handled with a term on its own and leave typeStatus for the status of the type only. The term name itself is also used by ABCD: http://wiki.tdwg.org/twiki/bin/view/ABCD/AbcdConcept0603." The proposal is as follows: Definition: The scientific name that is based on the type specimen. Comment: It is recommended to also indicate the typeStatus of the specimen. Refines: Has Domain: Has Range: Replaces: ABCD 2.06: DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeDesignation/TypifiedName

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