This page shows the current state of integrations between Pensoft publication platforms and GloBI. This integration originated as part of developing a biodiversity-related knowledge hub on COVID-19 via COVID19-TAF - Communities Taking Action, a community-rooted initiative raised jointly by CETAF and DiSSCo.
These integration are very much a work in progress and will hopefully lead to an increased visibility of Pensoft publications that make claims about species interactions.
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events / integration status / integration profiles / translation tables / supported biotic interaction terms
Events
16 April 2020 - Exploratory Pensoft<>GloBI integration meeting with Jorrit, Lyubo, Mariya. meeting notes .
23 April 2020 - Publication of Lyubomir Penev, Mariya Dimitrova, Viktor Senderov, Georgi Zhelezov, Teodor Georgiev, Pavel Stoev, & Kiril Simov. (2020). OpenBiodiv Archive (Version 0.0.1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3763429
18 May 2020 - Continued Pensoft<>Plazi<>GloBI integration meeting with Jorrit, Lyubo, Mariya, Donat, Guido, Teodor, Georgi. meeting notes .
25 June 2020 - Continued Pensoft<>Plazi<>GloBI integration meeting with Mariya (organizer), Jorrit, Lyubo, Donat, Georgi. meeting notes .
13 July 2020 - Continued Pensoft<>Plazi<>GloBI integration meeting with Mariya (organizer), Lyubomir, Georgi, Guido, Jorrit. meeting notes .
17 July 2020 - Mariya published blog post “Pensoft – GloBI workflow for FAIR data exchange and indexing of biotic interactions locked within scholarly articles” at https://blog.pensoft.net/2020/07/17/pensoft-globi-workflow-for-fair-data-exchange-and-indexing-of-biotic-interactions-locked-within-scholarly-articles/.
11 Aug 2020 - Mariya submitted abstract “Semantic Publishing Enables Text Mining of Biotic Interactions” to virtual TDWG 2020 annual conference Oct 19-23 2020.
12 Oct 2021 - Pensoft - Naturalis - GloBI meeting with Mariya Dimitrova (Pensoft), Lyubomir Penev (Pensoft), Teodor Georgiev (Pensoft), Georgi Zhelezov (Pensoft), Niki Kyriakopoulou (Naturalis), Jorrit Poelen (GloBI) discussing a possible collaboration to improve ways to extract (and predict) species interaction data from conserved/published materials like tables, specimen records. See meeting notes for more details.
Integration Status
Click on badges to browse/download indexed records or inspect automated reviews.
| status | institution/collection | platform | contact |
|---|---|---|---|
   |
Pensoft / Pensoft OpenBiodiv / Automatic discovered tables via OpenBiodiv | openbiodiv | Lyubo; Mariya |
 |
Pensoft / Pensoft tdb / Manually transcribed tables from Pensoft publications | arpha-table | Lyubo; Mariya |
 |
Pensoft / Pensoft tdb / DwC from Pensoft publications | arpha-dwc | Lyubo; Mariya |
 |
Pensoft / Pensoft tdb / Pensoft IPT | arpha-ipt | Lyubo; Mariya |
Integration Profiles
Integration profiles are descriptions on how data flows from one system to the next.
OpenBiodiv
| OpenBiodiv | GloBI Integration Profile |
|---|---|
| authors | ? |
| actors | ? |
| integration method | GloBI uses OpenBiodiv sparql endpoint to query for publications using that contains species interactions (e.g., dwc:habitat fields). GloBI indexes resulting pensoft publications and taxonomic treatments. Now, Pensoft publications and plazi taxonomic treatments can be found via GloBI. |
| diagram | ? |
| examples | see related issue 483 |
Arpha Table
| Pensoft Arpha Tables | GloBI Integration Profile |
|---|---|
| authors | ? |
| actors | ? |
| integration method | GloBI queries Arpha (?) for tables that include Darwin Core Archive attachments. GloBI parses the DwC-A and indexes species interactions terms contained in them. Now, Pensoft publications and plazi taxonomic treatments can be found via GloBI. |
| diagram | ? |
| examples | see related issue 481 |
Arpha DwC
| Pensoft Arpha DwC-A | GloBI Integration Profile |
|---|---|
| authors | ? |
| actors | ? |
| integration method | GloBI queries Arpha (?) for publications that include Darwin Core Archive attachments. GloBI parses the DwC-A and indexes species interactions terms contained in them. Now, Pensoft publications and plazi taxonomic treatments can be found via GloBI. |
| diagram | ? |
| examples | see related issue 480 |
Interaction Types
Supported Terms
Translation Tables
GloBI uses a subset of biotic interaction (or association) terms defined in the OBO Relations Ontology (OBO RO) to help classify and index biotic associations in collection records. Verbatim association types (e.g., on, parasite of, found on) are explicitly mapped into these OBO RO terms using translation tables. GloBI keeps a default translation tables and specific collection may choose to provide their own (see e.g., INHS-Insects ).
| resource | description |
|---|---|
| OBO Relations Ontology project page | OBO RO contains many kinds of terms, not just biotic associations terms |
| List of OBO RO Biotic Interaction Terms with definitions | a table of RO biotic interaction terms and their definitions (if available) |
| List of GloBI Supported Interaction Terms | subset of RO interactions terms that GloBI uses for indexing |
| Default Verbatim Terms Translation Table | the translation table used by GloBI to maps verbatim interaction terms to supported interaction terms |
| Example of Custom Verbatim Terms Translation Table | if provided/needed, GloBI can use a custom mapping provided by a collection |
The OBO RO is far from complete and we expect to add new terms and improve definitions as needed. Also, GloBI translation tables can be easily updated when needed. Please open an issue if you have questions or suggestions.
