[Taxacom] Tracking usages of biological collections, environmental terms and species traits in prospective publishing

Lyubomir Penev lyubo.penev at gmail.com
Fri Aug 21 08:04:06 CDT 2015

Dear Taxacomers,

​In the course of experimental testing of novel ways for increasing
machine-readability and semantic enrichment of taxonomic papers, we have
published the pilot paper
A new genus and species of dalodesmid millipede from New South
​ ​
Wales, Australia (Diplopoda, Polydesmida, Dalodesmidae)

There are two new buttons top right when opening the paper: InstCode
 and Terms

If one presses on the InstCode
 button, a list of institutional codes used in the paper and their usages
across the text and per taxon treatment appears in the right panel. The
full names of institutions are linked to
​the Global Registry of Biological repositories (​ <http://grbio.org/>
<http://grbio.org/>. If you press on the taxon treatments icon (the big "T"
icon), you
​will ​
get a list of taxon treatments that contain the respective institutional

​Similarly, ​by pressing on the
one will get lists of environmental terms and some morphological traits,
life cycle stages and some other terms, marked up against three exemplar
ontologies, the BRENDA Tissue Ontology, Disease Ontology and Environment
Ontology  (available for tagging via  https://extract.hcmr.gr/ > Help >

While tracking usage of collections and associate statistics seems more
than welcome to collection managers and their institutions, it is not so
obvious with markup of environmental terms and species traits  yet. This is
because we still lack extensive ontologies and vocabularies which will help
to build knowledge bases across different domains (or taxa in our case).

Nonetheless, linking of environmental terms, morphological and biological
traits to taxa in the narrative still during the publication process would
allow in the future to automatically harvest a lot of useful information
from the article text. Therefore, I am posting this message to seek for
some feedback on this first pilot.

The workflow was developed in a close collaboration with the Hellenic
Centre for Marine Research (HCMR) Crete, and Plazi during a workshop,
supported by the EUBON  <http://eubon.eu/>project.

​Feedback will be mostly appreciated. Please write me in person, if you
wish so, to avoid swamping of Taxacom.


Dr. Lyubomir Penev
Managing Director
Pensoft Publishers
13a Geo Milev Street
1111 Sofia, Bulgaria
Fax +359-2-8704282
ww.pensoft.net <http://www.pensoft.net/journals>
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