- tdwg-content - lists.tdwg.org

magnification/extent of objects present in images
by Steve Baskauf 03 Apr '13

03 Apr '13

I am cross-posting this to the Live Plant Image email list in addition to tdwg-content because this is a subject that was previously discussed there. However, as this is part of the public review of the draft Audubon Core TDWG standard, I would request that you reply only to the tdwg-content list, so that any additional discussion will take place there for the record. If you aren't on that list and would like to reply, please send your responses to steve.baskauf(a)vanderbilt.edu and I will post it for you. This subject came up as part of a comment on Audubon Core from Andréa Matsunaga: "In iDigBio (http://tinyurl.com/MISC-Media) some people have expressed the desire to have information about the magnification being used (to have a rough idea of the size of the object, potentially from data that is automatically retrieved from the capturing device) as well as the real world size depicted by a pixel (for the purposes of allowing one to make measurements on the image; this would require one to have a scale on an image and perform some arithmetic). Would it be possible to add such terms?" There are terms in the SpatialMetrics terms (section 9.1) of the MIX vocabulary (http://www.loc.gov/standards/mix/ ) that can encode this kind of information. However, I would be interested in opinions about whether expressing this kind of information is a narrow need that is outside the scope of a fairly broad standard like Audubon Core or if the need for such terms is perceived as widespread. Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu

1 0

AC Comment: terms for phylocode and DNA barcode
by Steve Baskauf 25 Mar '13

25 Mar '13

Rob Stevenson made another helpful comment with regards to the proposed Audubon Core standard: "Rather than have Term Name: associatedSpecimenReference as a place for phylocode and a DNA barcode, should the standard support specific fields for a phylocode and a DNA barcode? These seem to be independent approaches that might help anchor or tie together multimedia observations. I can image people taking a picture of an insect and getting a DNA barcode but not having a Taxon Name or a set of characters completed. It seems that molecular data are becoming more and more important and their collection is becoming more and more automated. For microbes, molecular characterization seems to be the main approach uses". I have not opened an issue for this item because although it is an important issue, I'm not sure it is in scope for Audubon Core. AC imports terms from other vocabularies when possible (notably Darwin Core), but generally only mints terms when they deal specifically with multimedia and when existing vocabularies don't already provide such a term. The issue that Rob raises is a general one that needs to be discussed in the context of how vocabularies such as Darwin Core (which are currently designed primarily to facilitate "flat", specimen-oriented databases) can be adapted for use in more normalized databases which integrate information about many kinds of resources (e.g. specimens, DNA sequences, images, etc. ). This is a topic that is the subject of ongoing discussions with groups such as BiSciCol, RCN4GSC, and the TDWG RDF task group. But it may be too much for Audubon Core to take on at this point in time. Opinions? Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu

1 0

AC Comment: opened new issues
by Steve Baskauf 25 Mar '13

25 Mar '13

Rob Stevenson has provided several useful comments regarding the proposed Audubon Core standard. I have opened two issues related to his comments: Issue 45 (http://code.google.com/p/auduboncore/issues/detail?id=45 ) to include LTER Datasets controlled vocabulary for CVterm term. Issue 46 (http://code.google.com/p/auduboncore/issues/detail?id=46 ) which combines Alexey Zinovjev's earlier comment with a comment from Rob regarding specifying multiple taxa related to a media item: "Let's say I have a picture of a leaf with holes in it. Is there a way to specify the taxon of the leaf and the taxon of the insect that made the holes. Caterpillar species A eats Plant leaf Species B? If I know that caterpillar only made that shape hole when it was parasitized can I also specify the taxon of the parasite? Another leaf example would be lichens and liverworts that colonize leaves. One might be over growing another? In general I would like to specific multiple taxa and relationships among the taxa in the image or movie, etc" Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu

1 0

Audubon Core Review: media recording traces of organisms
by Steve Baskauf 24 Mar '13

24 Mar '13

Here is a forward of a question I received regarding the Audubon Core term list: The immediate question: How would I record most of my sawfly photos: which are usually not sawflies [adults or larvae] themselves but their galls, mines, 'holes in leaves' (sometimes, by their shape, I can precisely identify species produced it), etc., etc. People will photograph nests, animal's traces, record bird songs, but how such media would be tracked? It seems to be a very common situation. I did not notice anything for such "product" instead of animal itself. I should have seen a generic term somewhere but don't remember neither the English or Latin word nor where could I see it. Alexey -- azinovjev(a)fastmail.fm

1 0

reminder about the Audubon Core public review (ending April 1)
by Steve Baskauf 23 Mar '13

23 Mar '13

Please note that the end of the public review period for the Audubon Core Multimedia Resources Metadata Standard is near (April 1). The call for public review, which includes links to the proposal and instructions for commenting, can be viewed at http://terms.gbif.org/wiki/Audubon_Core_1.0_Call_For_Public_Review . If you would like to comment but don't want to figure out how to use the issue tracker, you may also send your comments directly to me at steve.baskauf(a)vanderbilt.edu and I will post them for you. Steve Baskauf Audubon Core review manager -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu

1 0

Review of TDWG ontologies and DwC namespace policy
by Steve Baskauf 13 Mar '13

13 Mar '13

The Vocabulary Management task group (VoMaG) is soliciting input for a report with recommendations for future action on the part of TDWG. I have been co-opted to organize contributions to the report on the topic of the status of the TDWG ontologies and a review of the Darwin Core namespace policy. In particular, what (if anything) should be done with the TDWG ontologies and should the Darwin Core namespace policy (i.e. the mechanism for amending Darwin Core) be adopted in some form as a model for all TDWG voabularies? If you have opinions or suggestions that you would like to contribute, you can do so at the VoMaG site. The task group entry page is at: http://community.gbif.org/pg/pages/view/30603/ The background summary on the TDWG ontologies and DwC namespace policy is at: http://community.gbif.org/pg/pages/view/29079/ which has a link to the page for discussion. If you find the wiki format to be a barrier, you can also email comments directly to me. The timeline for moving the report forward has a March 31 deadline for contributions, so if you have thoughts on the subject, please assemble them by the end of the month. Thanks, Steve Baskauf -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

1 0

Audubon Core Public Review
by Steve Baskauf 02 Mar '13

02 Mar '13

(Apologies for any cross-listing) Audubon Core Public Review By: Steve Baskauf, Review Manager Biodiversity Information Standards (TDWG) announces the Public Review of the proposed Audubon Core Multimedia Resources Metadata Standard. Audubon Core is designed to provide a controlled vocabulary to address the management, acquisition, and content descriptions of biodiversity multimedia. It is a product of the Joint GBIF- TDWG Multimedia Resources Task Group (MRTG) and has undergone peer review, several revisions, and review by the TDWG Executive Committee. If you are a potential producer or consumer of metadata for biodiversity-related multimedia, we would like your input on this proposed TDWG Technical Specification Standard. You may find it easiest to view the proposed standard online. The following links lead to the three parts of the standard: - the non-normative introduction: http://terms.gbif.org/wiki/Audubon_Core_Non_Normative_Document - the normative introductory material: http://terms.gbif.org/wiki/Audubon_Core_(1.0_normative) - the normative term list: http://terms.gbif.org/wiki/Audubon_Core_Term_List_(1.0_normative) A downloadable zip archive containing the proposed standard can be obtained at http://www.tdwg.org/standards/638/ . This archive includes an informative adoption and sustainability plan which is not an official part of the proposed standard. To raise specific issues or to make specific recommendations, use the issues tracker described at http://code.google.com/p/auduboncore/wiki/AboutIssueTracker . To engage in general discussion about the standard, join the TDWG email list (tdwg-content) by subscribing at http://lists.tdwg.org/mailman/listinfo/tdwg-content . You can then post messages to tdwg-content(a)lists.tdwg.org . Issues raised in that conversation may be added to the issue tracker as well. Comments about the proposed standard will be archived as a part of the standards adoption process. In accordance with the TDWG standards process, a minimum of 30 days is required for public comment on the proposed standard. Comments should therefore be received by 1st April 2013. For more information about the TDWG standards process, see http://www.tdwg.org/standards/status-and-categories/ and http://www.tdwg.org/about-tdwg/process/ . Please distribute this call for comment to anyone you think could or should comment on Audubon Core. You may address any questions about the review process to me at steve.baskauf(a)vanderbilt.edu . Thanks to the authors, Robert A. Morris (convenor), Vijay Barve, Mihail Carausu, Vishwas Chavan, Jose Cuadra, Chris Freeland, Gregor Hagedorn, Patrick Leary, Dimitry Mozzherin, Annette Olson, Greg Riccardi, and Ivan Teage for their work on the proposed standard. Thanks also to the anonymous reviewers, the Executive Committee, and Lee Belbin who served previously as Review Manager for the standard.

1 0

Open Annotation Ontology Rollout
by Bob Morris 15 Feb '13

15 Feb '13

The W3C Open Annotation Community Group <http://www.w3.org/community/openannotation/> is pleased to announce three public meetings introducing the Open Annotation Data Model Community Specification. The Open Annotation Core Data Model <http://www.openannotation.org/spec/core/> specifies an interoperable framework for creating associations between related resources, annotations, using a methodology that conforms to the Architecture of the World Wide Web. Open Annotations can easily be shared between platforms, with sufficient richness of expression to satisfy complex requirements while remaining simple enough to also allow for the most common use cases, such as attaching a piece of text to a single web resource. These day-long public roll-outs, carried out in concert with the Annotation Ontology and the Open Annotation Collaboration, and made possible by generous funding from the Andrew W. Mellon Foundation, will inform digital humanities and sciences computing developers, curators of digital collections and scholars using digital content about the W3C Open Annotation Community Group’s work. Participants will learn about the data model's core features and advanced modules through tutorials, a showcase of existing implementations, Q&A sessions with community implementers and live demonstrations. Topics will include: * The Open Annotation Data Model * The W3C Open Annotation Community Group * Existing implementations * Developer tools & resources Rollout times and locations: * U.S. West Coast Rollout – 09 April 2013 at Stanford University Registration: <https://www.eventville.com/Catalog/EventRegistration1.asp?Eventid=1010270> * U.S. East Coast Rollout – 06 May 2013 at the University of Maryland Registration: <https://www.eventville.com/Catalog/EventRegistration1.asp?Eventid=1010271> * U.K. Rollout – 24 June 2013 at the University of Manchester Registration: <https://www.eventville.com/Catalog/EventRegistration1.asp?Eventid=1010272) There is no registration fee but RSVP (online) is required. RSVP for a rollout near you using one of the links above. For more information and individual agendas, see: <http://www.openannotation.org/RolloutInfo.html> -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Harvard University Herbaria Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://wiki.filteredpush.org http://www.cs.umb.edu/~ram === The content of this communication is made entirely on my own behalf and in no way should be deemed to express official positions of The University of Massachusetts at Boston or Harvard University.

1 0

iDigBio Hackathon - Day 1 - Listen in 9AM - Noon CST
by Debbie Paul 13 Feb '13

13 Feb '13

Hi Everyone, Are you interested in digitization workflows for natural history museum collections that involve OCR, machine learning and natural language processing? iDigBio's first Hackathon starts this morning, Wednesday February 13th and begins with 10 minute lightning talks by participants sharing their results so far to parse OCR output. Participants will spend 2 days together sharing and tweaking algorithms aimed at making parsing OCR output better. Other big topics of the hackathon are image processing/segmentation/analysis and also the continued need for user-interface development for interacting with the OCR output (front-end human-in-the-loop and api interfaces). Tune in: http://idigbio.adobeconnect.com/augmentocr 9AM - to about noon CST. Read more at: http://tinyurl.com/aocrhackathonwiki Works better with Firefox (b/c of Flash). Headsets are a good idea for best sound. From all of us at the Hackathon, See you there. Deb

1 0

Announcing the VertNet Undergraduate Internship
by Russell, Laura 07 Jan '13

07 Jan '13

Call for Applications VertNet Undergraduate Internship VertNet is pleased to announce the VertNet Undergraduate Internship, scheduled for the Summer of 2013. This internship is an opportunity for two undergraduate students to gain valuable training and practical experience in biodiversity informatics, biodiversity research and systematics, and museum collection management. Two internship positions are available; one at the University of California, Berkeley, and one at the University of Colorado in Boulder. Internships will not exceed three months (12 weeks) and will include participation in VertNet’s Biodiversity Informatics Training Workshop in Boulder, Colorado, on June 24-28 (http://vertnet.org/about/BITW.php)<http://vertnet.org/about/BITW.php)>, as a part of the Interns’ training. Who should apply? We welcome applications from eligible student from within the United States and U.S. Territories interested in pursuing a biodiversity informatics project while exploring the practice of science as conducted at a natural history museum. Undergraduate students and students preparing to graduate in Spring 2013 are eligible to apply. We are interested in individuals who are self-motivated and can apply new tools and data resources creatively to questions of biodiversity, which may be in ecology, conservation, geography, evolutionary biology, environmental science, computer science, museums, or library and information science. Interns will work with the VertNet project team of experienced museum curators, researchers, and informaticists, as well as individuals from VertNet integration partners, such as AmphibiaWeb, Animal Diversity Web, and EOL, to design and conduct a research project that synthesizes and analyzes data from multiple biodiversity resources. These projects can be informatics-based, writing code and programming novel ways to analyze or display these kinds of data, or they can be biologically-focused, using data to answer questions about species diversity, ecology, evolution, or distributions. The internship will emphasize the creation, use, and analysis of aggregated biodiversity data from VertNet, and other sites, for research and data improvement and the contribution of data back to these sites. We expect research project to focus on assembling species dataset for use in spatial ecological modeling or global change biology. We are, however, open to other research topics and foci. Projects do not need to be fully realized at the time of application. Publication of the results from the internship is encouraged and will be supported by the VertNet team. Publication may take the form of web-based species accounts for VertNet integration partners, georeferencing species occurrence data, open-source software, or collaborations on other scientific publications. VertNet Project Team members (http://vertnet.org/about/team.php<http://vertnet.org/about/team.php)>) at CU Boulder include Robert Guralnick and Javier Otegui. Team members at UC Berkeley include Carla Cicero, Carol Spencer, Michelle Koo, David Bloom, John Wieczorek, and Aaron Steele. In addition to individual research project mentors, Interns will work with members of the VertNet Project Team and possibly other museum staff at both institutions to learn about daily operations of museum, and how those local activities tie into the larger perspective of global informatics. At the end of the internship, participants should have: 1. an understanding of the evolution of, and the workflows within, a research project; 2. basic skills and experience using data repositories, biodiversity informatics and analytic tools, and an understanding of which tools are appropriate for specific tasks; 3. an understanding of the operation and maintenance of a natural history collection; 4. knowledge of the abundant biodiversity resources and additional training available to them. Workshop Selection and Support Acceptance to the VertNet Undergraduate Internship is a competitive, nation-wide process and is limited to two (2) participants; one at UC Berkeley and one at CU Boulder. All applications materials and recommendations must be received by 11:59pm PT on January 11, 2013 for consideration. Accepted participants will be notified in March 2013. Individuals selected to participate will be considered full time employees of their respective institutions and paid at the monthly rate of $3150 (CUBoulder)/$3300 (UCBerkeley). Interns will receive additional support to cover costs during the workshop for travel between Berkeley and Boulder and accommodations and per diem (when in residence at the secondary institution). Interns will be responsible for their own travel to and from the internship and accommodations and daily needs while in residence at the primary institution. Support is available to help find accommodations in both locations. Application materials are available at <http://vertnet.org/about/BITW.php> http://www.vertnet.org/about/Internship.php. Submit all application materials online (http://www.vertnet.org/about/Internshipapplication.php) or send all completed materials and one letter of recommendation to dbloom(a)vertnet.org<mailto:dbloom@vertnet.org>. Laura Russell VertNet Programmer VertNet KU Biodiversity Institute 1345 Jayhawk Blvd. Dyche Hall, Room 606 Lawrence, KS 66045 Phone: +01 785 864-4681 Fax: +01 785 864-5335 email: larussell(a)vertnet.org email: larussell(a)ku.edu Skype: laura.anne.russell Gchat: larussell(a)vertnet.org url: www.vertnet.org

2 1