March 2019 - tdwg - lists.tdwg.org

CFP: Workshop on conceptual modeling in LAMS and data repositories
by andrea thomer 29 Mar '19

29 Mar '19

Hello, I'm co-organizing a workshop on the application of conceptual modeling in LAMS and data repositories, and would love to see some TDWG-y biodiversity informatics-y folks there. Happy to answer any questions about what kind of papers we're hoping to see. Call For Papers (full CFP: https://sig-cm.github.io/news/JCDL-CFP/) *Workshop Description* Advances in digital libraries, archives, museums and repositories have relied upon conceptual modeling efforts that provide formal representation information and identity conditions for digital resources. Examples include conceptual models traditional to library and information sciences, such as Functional Requirements for Bibliographic Records (FRBR), the uptake of data models from the semantic web, like the Resource Description Framework (RDF), as well as the development of protocols unique to the exchange of digital objects, such as the Open Archives Initiative for Object Reuse and Exchange (OAI-ORE). Sustaining this rich tradition of research and development in conceptual modeling requires a collective effort from the digital library community. This workshop focuses on critically evaluating and furthering existing conceptual models, as well as developing an agenda for future research and community-building around these topics. *Contributions* We seek contributions from practitioners and researchers interested in digital collections in different domains, especially collections built upon different conceptual models emerging from different epistemologies and different traditions of knowledge organization: natural history museums, art museums, library special collections, archives, data repositories, earth science informatics, biodiversity informatics, etc. This may include topics relevant to conceptual modeling, including but not limited to: - the history and evolution of conceptual models, - extensions to, or critiques of, existing conceptual models, - the development of domain-specific conceptual models (e.g. in the earth sciences, in the humanities, etc) applied strategies for modeling in development processes, - critical examination of the social and technical implications of conceptual models. Contributions may be of two varieties: - *Full research papers* should present results from completed research, or fully developed conceptual analysis. Full research papers should be a maximum of 3000 words in length (not including citations). - *Short research papers* can present in-progress work, small case studies, position statements, or theoretical and conceptual analysis that is at an early stage of development. Short research papers should be a maximum 1500 words in length (not including citations). *Dates* - Submission Deadline is April 25th - Notifications will be sent no later than April 29th - Accepted submissions can be revised before May 25th. At the time we will post all accepted submissions to the workshop website. - Workshop will take place June 6th. *Instructions for Submission* Please submit a PDF, DOC, or TXT document to nmweber(a)uw.edu by April 25th. You may use any format or citation style that you prefer - However, we do suggest following the conference’s ACM template <https://www.acm.org/publications/proceedings-template>. All Submissions will be reviewed by the organizing committee. *Organizing Committee* - Katrina Fenlon (kfenlon(a)umd.edu) University of Maryland - Peter Organisciak (peter.organisciak(a)du.edu) University of Denver - Andrea K. Thomer (athomer(a)umich.edu) University of Michigan - Nic Weber (nmweber(a)uw.edu) University of Washington

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Workshop Announcement “An Introduction to Anatomy Ontologies”, ZFMK Bonn, 8th May 2019
by Lars Vogt 22 Mar '19

22 Mar '19

*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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Workshop Announcement “Semantic Data Models in Anatomy”, ZFMK Bonn, 9th-10th May 2019
by Lars Vogt 22 Mar '19

22 Mar '19

*Workshop: 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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Position Announcement
by Rios, Nelson 01 Mar '19

01 Mar '19

Posting for a colleague: 3 OPEN POSITIONS (Software Engineer, Data Analyst, Mobile App Developer) The Map of Life project is seeking a Full-stack Software Engineer, Data Analyst, and Mobile App Developer to join our growing team of developers and scientists at Yale University in New Haven, Connecticut. Full details for each of the positions and how to apply can be found at: https://bgc.yale.edu/opportunities Thanks, Nelson Nelson E. Rios Head of Biodiversity Informatics and Data Science YALE PEABODY MUSEUM OF NATURAL HISTORY PO Box 208118, New Haven, CT 06520-8118 P +1 (203) 432-1844 peabody.yale.edu

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