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

Alex Thompson godfoder at acis.ufl.edu
Fri Aug 21 08:53:03 CDT 2015


Speaking as a technical person at iDigBio, this is great! This is 
exactly the kind of step forward that we think needs to happen to 
finally be able to collect some real statistics on data usage in 

I have two questions about this though:
1) Is there / are you planning on building an index page where we could 
direct collection managers to that shows papers by institution code.
2) Are you using GRBio data dumps as an authority file? If so, what are 
you doing about the <IH> labled institution codes from Index 
Herbariorum? Sometimes those will conflict an unrelated non-herbarium 

Alex Thompson

On 08/21/2015 09:04 AM, Lyubomir Penev wrote:
> 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)
> <http://zookeys.pensoft.net/articles.php?id=5913>.
> There are two new buttons top right when opening the paper: InstCode
> <http://zookeys.pensoft.net/articles.php?id=5913&display_type=list&element_type=15>
>   and Terms
> <http://zookeys.pensoft.net/articles.php?id=5913&display_type=list&element_type=16>
> .
> If one presses on the InstCode
> <http://zookeys.pensoft.net/articles.php?id=5913&display_type=list&element_type=15>
>   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/>
> ​io)
> <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
> code.
> ​Similarly, ​by pressing on the
>> Terms
> <http://zookeys.pensoft.net/articles.php?id=5913&display_type=list&element_type=16>
> button,
> 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 >
> http://tagger.jensenlab.org/GetEntities).
> 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.
> Cheers,
>> Lyubo
> ​mir​

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