Minutes of Workshop 1

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1. Workshop DFG project "eScience-compliant Standards for Morphology"

Burg Lenzen 2nd-4th of March 2015

Participants:

  • Roman Baum (ZFMK Bonn)
  • Patrick Beckers (Uni Bonn)
  • Philipp Bhatty (ZFMK Bonn)
  • Jan Decher (ZFMK Bonn)
  • Manfred Drack (Uni Tübingen)
  • Torben Göpel (Uni Rostock)
  • Peter Grobe (ZFMK Bonn)
  • Gregor Hagedorn (MfN Berlin)
  • Christian Köhler (ZFMK Bonn)
  • Sandra Meid (ZFMK Bonn)
  • Peter Michalik (Uni Greifswald)
  • Christian Montermann (ZFMK Bonn)
  • Michael Ohl (MfN Berlin)
  • Björn Quast (SuB Göttingen)
  • Friederike Saxe (MPKG Potsdam)
  • Thomas Stach (HU Berlin)
  • Lars Vogt (Uni Bonn)
  • Christian Wirkner (Uni Rostock)

Day 1

Welcome and introduction

Welcome address and introduction to the workshop by P. Grobe.

In groups of two participants each, the "personal questionnaire Day 1" was completed, followed by mutual introduction of each person to all participants.

Introduction: Ontologies

Presentation L. Vogt: "Einführung RDF, OWL, das Sematische Web und Triple Stores" (English: Introduction to RDF, OWL, the Semantic Web and triple stores). Download

Presentation T. Göpel: "Praxisbeispiel, morphologische Beschreibung anhand von Ontologiekonzepten" (English: Practical example, morphological description based on ontology concepts).

Discussion

  • Should hypotheses of homology be included in descriptions? This was rejected, because homology hypotheses are seen as a result of comparison and not as its prerequisite.
  • Basically, it will be possible to use multiple ontologies in a description in Morph⋅D⋅Base.
  • It has been discussed that the use of certain terms (fuzzy, curved) is problematic, because their textual definition is not always unambiguous, and thus different users will likely use them differently. In this context, the relevance of images (media in general) was discussed and how their use in and for ontologies could be improved. Perhaps, in cases like the one discussed, images can take the function of textual definitions?!?
  • In Morph⋅D⋅Base, images can increase the explanatory power of a description.
  • An additional glossary for the use of terms is not required, because the textual definitions and the formal class descriptions of ontologies provide this already (e.g., OBO).
  • The question regarding own ontologies arose. It was stressed that there are currently no plans to develop an ontology editor for use within Morph⋅D⋅Base. If for your own individual use cases ontologies need to be developed, this must be done outside of Morph⋅D⋅Base, using common editors such as Protegé (http://protege.stanford.edu/). It may be possible to offer a workshop with this topic at some point during the project phase.

Day 2

Status of the project

Presentation C. Köhler: „Eine kurze Einführung in das Projekt“ (English: A brief introduction to the project). Download

Discussion:

  • Ontologies are being created specifically for this project that control the application as well as the appearance and behavior of the interface of Morph⋅D⋅Base. This enables flexible generation of alternative web interfaces for future evaluation of their intuitive handling and operability by the use cases.
  • For storage, Morph⋅D⋅Base will use both a triple store (Jena triple store) and a relational database, the latter of which will be used to implemen for instance a messaging system.
  • Up to 28% of the cost of developing an application is required for the maintenance of the software systems. It was discussed that for the present project a partial financing is planned, consisting of future grant funding, budget and research projects of third parties.

Presentation P. Bhatty: „Erste graphische Entwürfe der GUI“ (English: Early graphic designs of the GUI). Download

Discussion:

  • For graphical representation of semantic graphs corresponding libraries can be used and adapted to Morph⋅D⋅Base.
  • The question arose: Should we question our own workflows based on the background of this project?
  • The ontologies that will be usable in Morph⋅D⋅Base also will be searchable and browsable within Morph⋅D⋅Base.
  • For purposes of comparison, the possibility of a matrix-like representation of formal descriptions was discussed (with possibilities for folding and blending in and out, etc.) and how such a representation could already be used when creating the descriptions.
  • Templates can be used for the generation of new entries, which will significantly increase the speed with which new data can be uploaded to Morph⋅D⋅Base.

Reports from the Use-Cases

Presentation J. Decher: „Taxonomic Descriptions and Digitization of Upper Guinea (West Africa) Crocidurine shrews from the ZFMK Collection“. Download

Discussion:

  • Desire to connect other systems (e.g. Diversity Workbench) to Morph⋅D⋅Base. This is possible in principle and exchange formats exist. However, mechanisms for authentication must be provided that apply to all systems involved, which is not trivial.

Presentation T. Göpel: „Evolutionäre Morphologie von Kreislaufsystemen bei Arthropoden“ (English: Evolutionary morphology of circulatory systems of arthropods). Download

Discussion:

  • Possibility to make descriptions at the level of individuals has been requested. It should generally be possible to make a description of any OTU, with a specification of whether this OTU represents an individual, a lot, or a taxon.

Presentation M. Ohl: „Taxonomy and Phylogeny of aculeate wasps“. Download

Discussion:

  • Important for taxonomic descriptions is the comparative diagnostic description and the non-comparative complete description. Wanted are full descriptions of species with ecological data include, etc.

Presentation F. Saxe: "Historical Struktures in the Laboratory". Work in progress - ask author for details.

Discussion:

  • Legacy data (historical literature) is to be reclaimed for today's materials science.

General discussion of the Use-Cases

  • About the web research of ontologies needed. The use cases cannot answer this question at this time.
  • The desire for interoperability of systems was expressed again.
  • The possibility of a comparative overview of several descriptions is desired.
  • The question of the nature of the reference of descriptions was intensively discussed again. The taxonomists emphasized that limiting this reference to individuals is not tenable for taxonomic, because higher-level descriptions (descriptions of taxa) are formally required. This results from the "genus et differentia" approach used in taxonomy: due to higher-level descriptions, several structures are already presumed and are no longer listed in species descriptions, as they are already covered by higher-level descriptions. Therefore, the proposal to use the concept of an OTU as a reference, which can then be further differentiated into specimen, series, lot or higher taxon (or even pseudo-specimen?).
  • Information that should be coverable for taxonomic descriptions: habitat, behavior, morphometrics.
  • Provenance data must be documented for the descriptions (valid for all use cases).
  • The import of data tables should be possible for Morph⋅D⋅Base.
  • Morph⋅D⋅Base's new 3D viewer was presented and several 3D object formats proposed (U3D, vrml, obj, x3d (om)).
  • It came to the question of whether barcodes can be saved in Morph⋅D⋅Base. Answer: Morph⋅D⋅Base is not a repository for barcodes.
  • It should be possible in Morph⋅D⋅Base to create templates for your own use for new descriptions, with identification of the fields yet to be processed/edited.
  • Desire for text mining on word frequencies, which could be interesting also for taxonomy. Goal for materials research: Being able to make facets on word frequency and word relationships.
  • We talked about the possibility of publication of descriptions from Morph⋅D⋅Base and collaboration with publishers: semi-automatic publication. What additional text boxes are necessary? What do publishers need to be able to publish from and with Morph⋅D⋅Base (Pensoft?).
  • It was discussed how the semantic approach for taxonomic descriptions will bring new ways of taxonomic work with it.
  • The question of different languages in taxonomic descriptions. Markup is initially in English, even with non-English texts

The participants are distributed to three groups: Morphology, Taxonomy, and Annotation

Day 3

Initial evaluation of the questionnaires

  • ontologies wanted
  • percentage overview of personal questionnaires
  • suggestions for improvement of the current version of Morph⋅D⋅Base
  • new knowledge and requirements
  • it is desired to be able to annotate individual triple statements during input (e.g. adding references, serial section numbers, an image, etc).

Visions: How would the research for morphologists / taxonomists be in an ideal world?

See also PDF for details.

  • Automatic annotation of image and 3D data
    • Structure and pattern recognition
    • Automatic 3D reconstruction, including segmentation => E.g. ICT Toolkit
  • Work & communication platform
    • Building on preliminary work; not having to always start over
    • Editors and reviewers have access to publications
  • Free accessibility and usability of data
  • Visualization of similarities
    • Quantification of similarities
    • Image-driven ontology-term generation
    • Automatic detection of missing term classes
    • Recognition of patterns, correlations and possible dependencies
  • Natural Language Processing
    • Natural-language-text to RDF
    • Historical texts, incl. Taxon-Finder
  • RDF to Image
    • Automatic reconstruction of e.g. shapes based on triple statements
    • Automatic generation of 3D schemes based on triple statements
  • Universally applicable taxonomy
    • Taxon-Finder
    • Complete and up-to-date
  • Data
    • Trust in data
    • High-quality data
    • Quality Index for data
    • Completeness
    • Material
    • Function
    • Structure
  • Universally applicable (Tablet?)

Outlook:

The programming team of the project will not develop any anatomy ontologies. However, we can organize a workshop about learning methods and tools for developing ontologies. We will discuss whether we invite additional ontology experts for such a workshop. The participants asked for the next workshops for a more practical approach, including the input of triple statements into a web interface. The interface will be discussed further during future workshops. Designs will be presented and optimized for the workflow of the use-cases. In the future there will be regular meetings (e.g. using Skype). Participants: Developers and one use case. When: e.g. every 2-3 months. The current status of the project is documented in the Wiki (emorphology.morphdbase.de). This is also the site in which we will document our workshops and provide the presentations we got from you.