- tdwg-content - lists.tdwg.org

another typo; acronym expansion; list pointing
by Gail Kampmeier 08 May '09

08 May '09

Dumbledore was at work on this one: http://rs.tdwg.org/dwc/terms/namespace/index.htm "Darwin Dore Namespace Policy" as the big title!!! :-D Also, first use of URI should be expanded on this page to Uniform Resource Identifier http://en.wikipedia.org/wiki/URI (link may or may ot be desirable). 3.2 Substantive editorial errata - the link to [DWC-MAIL] brings up whether you want to take the user to a page to subscribe to the mailing list or link to a blank outgoing email, which I presume you must be a subscriber to send...? [from earlier email: On http://rs.tdwg.org/dwc/index.htm Participation: [DWC-MAIL] link should not just open a blank email (such as this one) but go to http://lists.tdwg.org/mailman/listinfo/tdwg-content so that people might subscribe. Differentiates from sending mail to the mailing list in the list References (and perhaps elsewhere). ] I would argue that rather than using a mailto that this link http://lists.tdwg.org/mailman/listinfo/tdwg-content allows users to subscribe OR send a message from there. I guess you don't have to subscribe to send an email to the list...does this ever get abused? Whether other mailing lists should be similarly listed may need to be visited. Gail

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Comment links usually 404
by Gail Kampmeier 08 May '09

08 May '09

I'm on http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm and notice that most of the comment links 404 (likely on other pages too with terms). Would it be better to either create placeholders for each term for content for these or how will the user figure out how to start adding information? Gail

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typos? and notes on the issue tracker
by Gail Kampmeier 08 May '09

08 May '09

Have tried using the issue tracker and see that it leaves things anonymous (#23). I don't know whether the DwC authors can see/contact users leaving comments/issues outside of this forum, whether the anonymity disappears when someone related to the project takes on solving the issue....? If this will be of more heavy duty use, a bit more documentation on expectations may prove useful to non-power users. As for the typos, on http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm in the Abstract, the dcterms:type">dcterms:type and basifOfRecord terms contain one known typo and another probable typo in that which is highlighted. Also, did you mean for the document, "Darwin Core Terms: A complete history." to be a link in the abstract to I presume http://rs.tdwg.org/dwc/terms/history/index.htm --might be helpful since the left nav link title is truncated form of this, although I guess it is questionable if you want users going there from this page...? Gail

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issue tracker?
by Gail Kampmeier 08 May '09

08 May '09

Regarding the message sent last night on using this list for the public review, I have now run into another prospective method on http://code.google.com/p/darwincore/ --the "Issue Tracker" but it has no link... where is this? Is this it http://code.google.com/p/darwincore/issues/list ? Is it suitable for public review or should this be more internal to your working group? Would you rather I be using something other than this list to post questions? I know John is in the field, but please someone else jump in if you can help. I am hoping to send this to the Exec once I finish going through it myself. Thanks! Gail Review Manager, DwC

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XML document display
by Gail Kampmeier 08 May '09

08 May '09

I am on http://rs.tdwg.org/dwc/terms/simple/index.htm My normal browser of choice is Safari (currently 3.2.1), which does not display XML (in fact comes up as a blank page) as in http://rs.tdwg.org/dwc/examples/text/example_text_simpledwc_complete.xml I took this to Firefox 3 and it displayed fine. Opera 9.64 is similar to Safari (=blank). Do we need to state up front that this is best displayed in Firefox for XML (and if I recall anything in RDF?) or indicate that if you View as Source, you can see the XML as it was intended? This caveat may need to be shown on any page referencing such pages. By the way, have I told you lately how impressed I am with the revised version?! Cheers! Gail

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participation & pubic comment mechanism
by Gail Kampmeier 07 May '09

07 May '09

On http://rs.tdwg.org/dwc/index.htm Participation: [DWC-MAIL] link should not just open a blank email (such as this one) but go to http://lists.tdwg.org/mailman/listinfo/tdwg-content so that people might subscribe. Differentiates from sending mail to the mailing list in the list References (and perhaps elsewhere). This now answers how we are going to make it easy for the public review to be able to comment, right? Do we need to give instructions about referencing the URL concerned in the message or is this stating the obvious? One potential problem with using this during the public review phase will be that everyone subscribing will get all of the posts such as this one. Is there a better way to handle this? Otherwise the new introduction is looking good! Gail

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Darwin Core review
by Peter Desmet 07 May '09

07 May '09

Hi everyone, As Marküs informed me last time, I should post all my Darwin Core remarks on this list. Most of my remarks are about missing information in the complete historical record (see below), except the following: 1. Great work!! I haven't had time to read the full documentation yet, but I'm very glad everything is so well documented now. It answers a lot of questions and it will greatly facilitate the adoption of the standard. Over the last 2 years I have given several presentations about Darwin Core to data publishers, but with all the current improvements, it will be a blast to do this! Especially the use of classes (instead of core and extentions) makes it much easier to grasp conceptually. 2. Is Darwin Core now officially in public review? Will we receive an invitation email to review (which I could forward)? 3. What is the reasoning behind changing all the term names from UpperCamelCase to lowerCamelCase? 4. HABITAT http://rs.tdwg.org/dwc/terms/index.htm#habitat > I don't think I agree the best practice for this term is to use a controlled vocabulary. This field can contain plenty of text information that may be lost if one switches to a controlled vocabulary. 5. GEODETICDATUM http://rs.tdwg.org/dwc/terms/index.htm#geodeticDatum > So you need to use the same geodetic datum for the verbatim coordinates as for the decimal lat & long? 6. PREVIOUSIDENTIFICATIONS http://rs.tdwg.org/dwc/terms/history/index.htm#previousIdentifications-2009… > Under the current definition (and examples) of previousIdentifications, this list can include person names and dates. This is significantly different from the previous definition: "A list (concatenated and separated) of previous ScientificNames to which the sample was identified". In my opinion this old definition should be kept in the complete historical record, with a "replaced by" link. ------------ MISSING/INCORRECT INFORMATION ------------ 1. The following historical classes cannot be found (anymore) in the complete historical record. If added, they should have a "replaced by" link and the new term should have a "replaces link" (except if new term is part of Dublin Core). > Sample (now http://rs.tdwg.org/dwc/terms/history/index.htm#Occurrence-2009-04-24) > SamplingEvent (now http://rs.tdwg.org/dwc/terms/history/index.htm#Event-2008-11-19) > SamplingLocation (now http://rs.tdwg.org/dwc/terms/history/index.htm#Location-2009-04-24) > SampleAttribute (now http://rs.tdwg.org/dwc/terms/history/index.htm#MeasurementOrFact-2009-04-24) > EventAttribute (now http://rs.tdwg.org/dwc/terms/history/index.htm#MeasurementOrFact-2009-04-24) > AccessConstraints (now http://dublincore.org/documents/dcmi-terms/#terms-accessRights) > Generalizations (now http://rs.tdwg.org/dwc/terms/history/index.htm#dataGeneralizations-2009-04-…) > SampleRemarks (now http://rs.tdwg.org/dwc/terms/history/index.htm#occurrenceRemarks-2009-04-24) > SamplingEventID (now http://rs.tdwg.org/dwc/terms/history/index.htm#eventID-2009-04-24) > SamplingEventRemarks (now http://rs.tdwg.org/dwc/terms/history/index.htm#eventRemarks-2009-04-24) > SamplingEventAttributes (now http://rs.tdwg.org/dwc/terms/history/index.htm#dynamicProperties-2009-04-24) > SamplingLocationID (now http://rs.tdwg.org/dwc/terms/history/index.htm#locationID-2009-04-24) > SamplingLocationRemarks (now http://rs.tdwg.org/dwc/terms/history/index.htm#locationRemarks-2009-04-24) > SamplingAttributeID and EventAttributeID (now http://rs.tdwg.org/dwc/terms/history/index.htm#measurementID-2009-04-24) > SamplingAttributeType and EventAttributeType (now http://rs.tdwg.org/dwc/terms/history/index.htm#measurementType-2009-04-24) > SamplingAttributeValue and EventAttributeValue (now http://rs.tdwg.org/dwc/terms/history/index.htm#measurementValue-2009-04-24) > SamplingAttributeAccuracy and EventAttributeAccuracy (now http://rs.tdwg.org/dwc/terms/history/index.htm#measurementAccuracy-2009-04-…) > SamplingAttributeUnit and EventAttributeUnit (now http://rs.tdwg.org/dwc/terms/history/index.htm#measurementUnit-2009-04-24) > SamplingAttributeDeterminedDate and EventAttributeDeterminedDate (now http://rs.tdwg.org/dwc/terms/history/index.htm#measurementDeterminedDate-20…) > SamplingAttributeDeterminedBy and EventAttributeDeterminedBy (now http://rs.tdwg.org/dwc/terms/history/index.htm#measurementDeterminedBy-2009…) > SamplingAttributeRemarks and EventAttributeRemarks (now http://rs.tdwg.org/dwc/terms/history/index.htm#measurementRemarks-2009-04-24) 2. There are plenty of missing discussion pages on the Google Code website. See attachment for full list. 3. See remarks per term. OCCURENCE http://rs.tdwg.org/dwc/terms/index.htm#Occurrence > Details links to 2008-11-19, not to the more recent 2009-04-24. http://rs.tdwg.org/dwc/terms/history/index.htm#Occurrence-2009-04-24 > Date modified: 2008-11-19? > No "replaces" link to 2008-11-19 http://rs.tdwg.org/dwc/terms/history/index.htm#Occurrence-2008-11-19 > Date modified: 2008-04-24? > Status: recommended? > No "replaced by" link to 2008-04-24 ----- LOCATION http://rs.tdwg.org/dwc/terms/history/index.htm#Location-2009-04-24 > Status: recommended? > No "replaced by" link to dcterms:Location ----- TAXON http://rs.tdwg.org/dwc/terms/index.htm#Taxon > Details link to 2008-11-19, not to the more recent 2009-01-23. http://rs.tdwg.org/dwc/terms/history/index.htm#Taxon-2008-11-19 > No "replaced by" link to 2009-01-23 > Status: recommended? http://rs.tdwg.org/dwc/terms/history/index.htm#Taxon-2009-01-23 > No "replaces" link to 2008-11-19 ----- INFORMATIONWITHHELD Some of the examples in http://rs.tdwg.org/dwc/terms/index.htm#informationWithheld are better placed in http://rs.tdwg.org/dwc/terms/index.htm#dataGeneralizations ----- RELATEDINFORMATION http://rs.tdwg.org/dwc/terms/history/index.htm#RelatedInformation-2007-04-17 > No "replaces" link to http://rs.tdwg.org/dwc/terms/history/index.htm#RecordURL-2005-07-10 ----- CONDITION http://rs.tdwg.org/dwc/terms/index.htm#reproductiveCondition > The reproductive condition of the biological individual(s): should include plural? ----- BEHAVIOR http://rs.tdwg.org/dwc/terms/history/index.htm#behavior-2009-04-24 > The decision (http://rs.tdwg.org/dwc/terms/history/decisions/index.htm#Decision-2009-03-0…) mentions SamplingEvent and Sample, two now historical classes. ----- CATALOGNUMBERNUMERIC http://rs.tdwg.org/dwc/terms/history/index.htm#CatalogNumberNumeric-2003-06… Is now historical, but there is no "replaced by" link (probably to: http://rs.tdwg.org/dwc/terms/history/index.htm#otherCatalogNumbers-2009-04-…) ----- EVENTDATE http://rs.tdwg.org/dwc/terms/history/index.htm#eventDate-2009-04-24 > Split the replaces link in two: EarliestDateCollected & LatestDateCollected ----- EVENTTIME http://rs.tdwg.org/dwc/terms/history/index.htm#eventTime-2009-04-24 > Split the replaces link in two: StartTimeOfDay & EndTimeOfDay ----- BINOMIAL http://rs.tdwg.org/dwc/terms/history/index.htm#binomial-2008-11-19 > Is not used in the DwC terms, but has the status: recommended. ----- RELATEDRESOURCETYPE http://rs.tdwg.org/dwc/terms/history/index.htm#relatedResourceType-2009-04-… > Is not used in the DwC terms, but has the status: recommended. ----- RELATEDBASISOFRECORD http://rs.tdwg.org/dwc/terms/history/index.htm#RelatedBasisOfRecord-2008-11… > Is not used in the DwC terms, but has the status: recommended. Regards, Peter -- Peter Desmet Biodiversity Informatics Manager / Directeur de l'informatique de la biodiversité Montréal Biodiversity Centre / Centre sur la biodiversité de Montréal Canadensys - www.canadensys.net Institut de recherche en biologie végétale Université de Montréal 4101 Rue Sherbrooke Est Montréal, Québec, H1X2B2 Canada Télé / Phone: 514-872-5249 Télécopie / Fax: 514-872-9406 Email: peter.desmet.cubc(a)gmail.com

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[tdwg-img] Multimedia Metadata Schema for public comment
by Robert A. (Bob) Morris 04 May '09

04 May '09

The Joint GBIF/TDWG Multimedia Resources Task Group (MRTG) invites discussion and critique of a draft metadata schema for biodiversity multimedia resources. The represention neutral was commissioned by GBIF and intended to be submitted to TDWG for acceptance along with proposed implementation,. The rationale for drafting such a standard is laid out in the "Non-normative document" linked at http://www.keytonature.eu/wiki/MRTG_Non_normative_document and in a set of recommendations MRTG made to GBIF in September 2008, also linked at the aforementioned wiki page. Briefly, the metadata standard proposes to extend several existing standards to provide deeper and broader utility than those provide. It seeks to make it easy for media providers using existing standards to leverage their current metadata services with an upward path to greater metadata granularity if they wish. The metadata schema also is designed to support the discovery and acquisition of multimedia resources for purposes beyond the traditional TDWG/GBIF use cases surrounding taxonomic inquiries and the documentation of taxon occurrence. These include use for species identification tools and ecological studies. We invite participation in the MRTG wiki at http://www.keytonature.eu/wiki/MRTG. It is not necessary to register for that wiki unless you desire to add contributions to it, which is the Task Group's preferred way of recording comments. We hope you have time to read the Non-normative document before commenting. The recommendations document will give the reader some insight into what social, technical, support, and outreach tasks would be required to make the schema useful by GBIF and others. Thanks in advance for your interest. My apologies if you see this announcement on several lists. Please feel free to forward to colleagues or lists you feel appropriate. Bob Morris Robert A. Morris Chair, MRTG Professor of Computer Science UMASS-Boston ram(a)cs.umb.edu http://efg.cs.umb.edu

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[tdwg-phylo] Reminder: Student application deadline for Summer of Code 2009
by Hilmar Lapp 29 Mar '09

29 Mar '09

*** Please disseminate widely to students at your institution. *** *** Note: Phylogenetics standards are among the project ideas *** *** and members of this Interest Group are among the mentors. *** PHYLOINFORMATICS SUMMER OF CODE 2009 - STUDENT APPLICATION DEADLINE IS APRIL 3 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program will receive a stipend from Google (and a T- shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Project ideas are listed on the website and range from hardware acceleration for phylogenetic inference, to support for phyloinformatics standards within the BioPerl and BioRuby toolkits, to alignment of next-gen sequencing data, to ontology term markup for biocuration, to semantic interoperability of web-services, to 3D-printing of phylogenies. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Instructions are at the website (see "When you apply"). You can find GSoC program rules and eligibility requirements at http://socghop.appspot.com . ***The 12-day application period for students ends on Friday, April 3rd, 2009, at 19:00 UTC (3pm EDT, 12pm PDT).*** INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early as possible. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

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[tdwg-phylo] Summer of Code 2009
by Hilmar Lapp 19 Mar '09

19 Mar '09

*** Please disseminate widely at your local institutions *** *** so that we reach as many students as possible. *** PHYLOINFORMATICS SUMMER OF CODE 2009 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http:// code.google.com/soc/) Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from hardware accerelation for phylogenetic inference, to tree visualization within a wiki, to alignment of next-gen sequencing data, to development of a reusable ontology term markup module for biocuration. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Apply online at the Google Summer of Code website (http:// socghop.appspot.com/) where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students opens on Monday March 23rd and runs through Friday, April 3rd, 2009. INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/ Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/ about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

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