April 2019 - tdwg - lists.tdwg.org

automated response
by Christy Semmens 26 Apr '19

26 Apr '19

Greetings. Thank you for your email. I am out of the country on a REEF project in Oman and will have little to no internet access from April 20 - May 5. I will respond as soon as I am able. If you need immediate assistance, please contact one of my colleagues at REEF (see http://www.REEF.org/about/staff) Thank you. Christy Pattengill-Semmens, REEF Director of Science

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Submission deadline for DCMI 2019 extended to 2019-05-17
by announce＠dublincore.net 26 Apr '19

26 Apr '19

The deadline for submissions to the programme of the The Dublin Core Metadata Initiative (DCMI) annual international conference has been extended to 2019-05-17. The DCMI conference this year will be hosted by the National Library of Korea in Seoul (23rd - 26th September, 2019) and promises to be a fantastic event! There is still time to submit a proposal: http://www.dublincore.org/conferences/2019/cfp/ This year we will also be running a Doctoral Forum[^1] and a Hack Day[^2] - see those respective web pages to find out how to contribute. Please consider submitting a proposal, and help to make this a conference to remember! Paul Walk (On behalf of the DCMI 2019 Programme Committee) [^1]: Doctoral Forum: http://www.dublincore.org/conferences/2019/doctoral_forum/ [^2]: Hack Day: http://www.dublincore.org/conferences/2019/hackday/

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Reminder for Workshop “Semantic Data Models in Anatomy”, ZFMK Bonn, 9th-10th May 2019
by Lars Vogt 18 Apr '19

18 Apr '19

We still have a few places available for our workshop “Semantic Data Models in Anatomy”, ZFMK Bonn, 9th-10th May 2019. Join us for two days of exciting talks and discussions on semantic data models in anatomy!* * * * *Workshop Announcement: Semantic Data Models in Anatomy * Morphological data are essential to a lot of research in the life sciences. They are usually published in form of unstructured texts. As a consequence, morphological data are neither FAIR (_F_indable, _A_ccessible, _I_nteroperable, _R_e-usable) nor computer-parsable, often hidden behind pay-walls, and struggle with the immanent semantic ambiguity of morphological terminology. Semantic technology such as knowledge graphs (e.g., ontologies, data graphs) provides a solution to these problems. However, in order to guarantee interoperability and comparability of morphological data, the morphological community must agree on common semantic data models for morphological data. Our experience with developing a semantic module for morphological descriptions for the morphological data repository Morph∙D∙Base (https://proto.morphdbase.de/) has shown that it is not easy to find such data models in the published literature. There is a need for publications that cover data models relevant to morphology. Currently, respective information is still scattered and not easy to find. The invited speakers will give an introduction to different approaches and data models for documenting anatomy in form of knowledge graphs. The workshop is intended to leave sufficient time for intensive discussions of the presented approaches and of new ideas brought up during the workshop. One of the goals of the workshop is to provide a starting point for collaboratively writing a paper that describes current approaches and models and discusses a comprehensive list of recommended concrete models together with rules when to apply them for semantically documenting various aspects of anatomy. Such a publication will help application developers to apply appropriate data models, help morphologists to produce reusable data, and will in general contribute to the overall integratability of morphological data. *_Speakers_* *James Balhoff*, University of Carolina, Chapel Hill, USA; *Meghan Balk*, Smithsonian Institution, Washington, USA; *Hong Cui*, University of Arizona, Tucson, USA; *István Mikó*, The Pennsylvania State University, University Park, USA; *Lars Vogt*, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany; *Matthew Yoder*, University of Illinois, Champaign, USA. *_Workshop Information_** Venue*Zoological Research Museum Alexander Koenig (ZFMK), Seminarraum (seminar room), Adenauerallee 160, 53113 Bonn, Germany* Start*9^th of May, 9am* End*10^th of May, 4pm *Registration*email to one of the workshop organizers (lars.m.vogt(a)googlemail.com; p.grobe(a)leibniz-zfmk.de);no registration fee applies *Reference to a preceding workshop*: On 8^th of May, a workshop on "An Introduction to Anatomy Ontologies <https://www.zfmk.de/de/forschung/tagungen-und-konferenzen/workshop-an-intro…>" will be held at the same venue. We are looking forward meeting you in Bonn, Lars Vogt & Peter Grobe --- Diese E-Mail wurde von Avast Antivirus-Software auf Viren geprüft. https://www.avast.com/antivirus

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Reminder for Workshop “An Introduction to Anatomy Ontologies”, ZFMK Bonn, 8th May 2019
by Lars Vogt 18 Apr '19

18 Apr '19

**We still have a few places available for our workshop “An Introduction to Anatomy Ontologies”, ZFMK Bonn, 8th May 2019. Join us for one day and get an introduction to the creation of anatomy ontologies.* * *An Introduction to Anatomy Ontologies* *Synopsis* This workshop is a brief introduction for researchers that are interested in formalizing how they formally represent the anatomy they study. Around half the content will cover what ontologies are, and how they can be used, the other half will focus on what concerns and issues arise when referencing anatomy in ontologies. The focus will be on existing ontologies and tools rather than future theoretical avenues, though resources of this type will be mentioned. The skeletomuscular system of arthropods will be used as an example. The workshop will be interactive, though most interactions will be discussion-based rather than tool based tutorials, this is a reflection of the available time. An honest, experienced appraisal of the pros-and cons of using ontologies for morphological research will be the cornerstone for discussion and questions. The workshop will be lead by Drs. István Mikó and Matt Yoder. *Logistics** Venue*Zoological Research Museum Alexander Koenig (ZFMK), Seminarraum (seminar room), Adenauerallee 160, 53113 Bonn, Germany* Start*8^th of May, 9am* End*8^th of May, 4pm* Requirement*Participants will need their own laptop with the software listed below /installed before the workshop/.* Registration*email to p.grobe(a)leibniz-zfmk.de or to lars.m.vogt(a)googlemail.com;no registration fee applies *Reference to a follow-on workshop*On 9^th to 10^th of May, a workshop on "Semantic Data Models in Anatomy <https://www.zfmk.de/de/forschung/tagungen-und-konferenzen/workshop-semantic…>" will be held at the same venue. *Target Audience* Researchers, or upper-level undergraduate to graduates whose research contains some component of morphology.No technical (computer/software) knowledge is required, though note that using ontologies is a technical exercise. Our overview will be conceptual rather than a deep dive. *Syllabus* *What is an Ontology? (what)* What is/not an ontology? Should you use ontologies?Why/not?Basic concepts: classes, instances, relationships (object properties), orthogonality, true-path, labels, URIs. Ontology formats, languages and syntaxes. *Anatomy and ontologies (why)* How ontologies are currently being used in current morphological research.Benefits. Design considerations: hierarchies and granularity.Best practices- definitions, reuse. Taking small steps: many vs. few relationships. *B**uilding and Curating ontologies - Software and Tools (how)* Building ontologies piecemeal, or extracting them automatically.Author driven vs annotator based ontologies. Ontology editors (OBO Edit. Protégé. Mx. Web-Protégé). An example ontology: skeletomuscular system of the insect thorax. *Formalizing morphology descriptions: from simple annotation to formal descriptions - (why and how)* Concepts for re-use and integration with tools such as Onto-fox and Noctua. Class based vs instance based formal descriptions. Manchester syntax. *Using ontologies as knowledge bases (when)* HAO, OaRCS. Flybase. Phenoscape. Quantitative analyses. *Community resources (who)* Listservs, tools, meetings. Other ontology courses, tutorials. Other experts creating and modifying ontologies. Next steps. **Software** Please have the following software install and/or visit websites prior to the workshop * Protégé - https://protegewiki.stanford.edu/wiki/Install_Protege5 * OARCS - http://oarcs.speciesfilegroup.org/projects/99/public/ontology_class/show_ex… * HAO - http://portal.hymao.org/projects/32/public/ontology/ --- Diese E-Mail wurde von Avast Antivirus-Software auf Viren geprüft. https://www.avast.com/antivirus

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