Talk:Concept Glossary

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synopsis of email discussion on uses and next steps

Arlin: the ConceptGlossary has matured into a unique resource! I am not aware of anything like this in books on phylogenetics, comparative genomics, etc. Currently it has over 100 terms, most of them defined. How can we promote and extend this unique resource in ways that benefit of the evolutionary analysis community?

  • add a copyleft license, so that textbook authors and teachers can use it?
  • what other projects could this serve?
  • who should know about this?
  • how can we ensure that the people who need this know about it?
  • how best do we incorporate the wisdom of the evolutionary analysis community?
  • should we add concrete examples to the definitions?
  • Something else?

Weigang: Somehow these terms needs to be grouped into categories, like in the GO, e.g.,

  • Tree descriptors: network-tree-nodes-OTU (graph theory terms?), root,
  • Character data descriptors: character matrix-character-state
  • OTU relations: polyphyla-paraphyla-monophyla, sister group, outgroup
  • evolutionary models

Arlin: yes, lets devise categories and sub-categories, but don't reformat the wiki page. Instead, incorporate statements describing relations into the definitions.


  • Should we not rather be having this discussion on wiki discussion pages (e.g. E-mailing design-stage discussions around is probably not a good idea.
  • The more I think about it, the more clear the need of a separate ontology for substitution models becomes to me. I can spawn atomic objects (e.g. a model parameter) and classes (e.g. substitution rate parameters or transition/transversion ratio parameters)

in my model descriptions. Hopefully this can be later rolled into a proper ontology. How flexible is Media Wiki in terms of exporting data to various formats?

Arlin: we can start storing a more complex representation, then flatten it out into a glossary with definitions. Anyone have ideas for technology to do this?

Rutger: I just read about Semantic Mediawiki which might be just what we need.

This discussion branched out toward substitution model description languages (below).

other glossaries (for comparison, learning, expanding term list)

The following page has links to many other pages not explored yet:

Sources examined already that overlap (probably not much more we can learn from these)

  • the glossary at the Paleos web site [1]
  • phylogenetics term list adapted from Hillis, et al. text [2]
  • UC museum of paleontology glossary of phylogenetics [3]

Sources to mine for additional concepts and relations:

  • glossary from PBS's Evolution series [4]
  • Ridley (Blackwell) Evolution textbook glossary [5]
  • glossary written from Strickberger's 2000 Evolution text [6] with hundreds of terms
  • _Life_ (WH Freeman) biology textbook glossary with over 1000 (est) terms [7]

Finally, some journals that publish numerous reviews and commentaries include glossaries that appear to be author-provided. This might be a useful source of definitions constructed by experts, e.g., the brief online glossary that accompanies a TREE review by Barrett and Schluter on adaptation from standing variation.