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BIII and Edam Bio Imaging
We deal with a wide variety of concepts and corresponding words in bioimage analysis. As BIII is intended to be a dictionary for bioimage analysis resources, use of terms and their definition should be shared within the community. Otherwise, we will likely to end up in many mis-understandings by each other, that lowers the usability of BIII itself. Occurence of such misunderstandings can be much higher in the interdiciplinary field where we use terms from computer science, biophysics, optics, machine regulations, biology and medicne.
To avoid the confusion in the usage of terms, we rely on the systematic and controlled naming of concepts we used- ontology.
EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioinformatics and computational biology, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of concepts with preferred terms and synonyms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use.
Edam Bioimaging is a part of EDAM Ontology project launched as a collaboration with the BIII project, and used for defining the vocabulary used in BIII in a hierarchical manner. Two major classes of Operation (Function) and Topics, as described in [BISE CORE ontology], which is the ontology used by BIII to define the fields of an entry (https://service.tib.eu/webvowl/#iri=https://raw.githubusercontent.com/NEUBIAS/bise-core-ontology/master/owl-ontology/bise-core-ontology-v1.1.owl) .
EDAM Bioimaging is accessible and editable on Bioontology.org (consultation) and on webprotege (suggestions for editions). These two sites have different roles: BioOntology site is for browsing the ontology, and WebProtege site is for adding new terms and to suggest updates of existing terms.
Operation class and Topic class are then reflected on Taxonomy called EDAM-Bioimaging-Topic and EDAM-Bioimaging-Operation. EDAM-Bioimaging-Format and EDAM-Bioimaging-Data are not used yet in BISE core ontology.
Matus Kalas is leading the update of EDAM Bioimaging ontology, which is an extension of EDAM ontology used in Bio.tools.
The taxonomy terms in BIII should be updated only when there is an official release. For this, a Python script called "biseEU_importer_taxonomy.py", done by Florian Levet, has to be run on a computer with Python 3.x installed. In addition, several modules have to be installed (argparse, urllib3, json, os, glob, csv, uuid, re, pymysql).
python.exe biseEU_importer_taxonomy.py -u <USERNAME> -p <PASSWORD> -td <WEBSITE> -i <TAXONOMY-FILE.TSV>
with
- <USERNAME>, the login of the administrator account of the drupal website
- <PASSWORD>, the password of the administrator account of the drupal website
- <WEBSITE>, the website address (e.q. https://test.biii.eu/)
- <TAXONOMY-FILE.TSV>, the path to the file containing the EDAM-bioimaging taxonomy in tsv format
Basically, the script reads every taxonomy entry of the EDAM-bioimaging file. Then it reads every taxonomy term of the Drupal site and compares them to the EDAM-bioimaging ones. If the taxonomy term is not in the Drupal site, it is created and added. If the taxonomy already exists, any change is updated in the Drupal site.
Actual state: The aim of the script was provide the ability to execute it from a personal computer. Unfortunately, OVH doesn't allow connecting to its database from outside the servers. We then need to upload the script to the server and execute it there. While Python is installed in the server, we need to add modules to it (urllib3, mysqldb), something we wannot do at the moment because we don't have access to the admin account of the OVH databases.
Testing on your local instance of Biii: In this case, you need to find the correct credentials to connect to the database. You can find them by executing
lando info
In the 'database' subpart, you will find 'creds' that will give you the user, password and database information. The 'external_connection' will give you the host and port information. Then you need to modify the following line in the script with the the personnal information of your installation:
Python 2.x
dbBise2_dev = MySQLdb.connect(host='localhost', port=32769, user='drupal8', passwd='drupal8', db='drupal8')
Python 3.x
dbBise2_dev = pymysql.connect(host='localhost', port=32769, user='drupal8', passwd='drupal8', db='drupal8')
Edam updating should be done in webprotege only. You can require an access from the link above. The additional keywords and biological terms suggested are regularly considered for synonyms or related terms , or main class, in Edam Bio Imaging. For rhis, this terms can be exported, or parsed with a list of software description having required them, by confirmed taggers role on BIII.