UniBioDicts: Unified access to Biological Dictionaries

John Zobolas; Vasundra Touré; Martin Kuiper; Steven Vercruysse

doi:10.20944/preprints202007.0586.v1

Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Version 1 : Received: 23 July 2020 / Approved: 24 July 2020 / Online: 24 July 2020 (13:48:50 CEST)

We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a search string, UBDs return a list of matching term, identifier and metadata units from databases (e.g. UniProt), controlled vocabularies (e.g. PSI-MI), and ontologies (e.g. GO, via BioPortal). This can be coupled to for instance the ‘vsm-autocomplete’ module: an input field (user-interface component) that offers autocomplete lookup for these dictionaries. UBDs create a unified gateway for accessing life science concepts, helping curators find annotation terms across resources (based on descriptive metadata and unambiguous identifiers), and data users search and retrieve the right query terms.

https://github.com/UniBioDicts: UniBioDicts GitHub-organization

https://vsmjs.github.io: Vsmjs project page

biocuration; dictionaries; ontologies; vocabularies; VSM

Your full name

Your affiliation information (e.g., name of your university/institution/organization)

Not displayed online.

Your Email address (not made public)

Please leave your comment to this article below.

Mathematical equations can be typed in either LaTeX formats \\[ ... \\] or $$ ... $$, or MathML format <math> ... </math>. Try the LaTeX or MathML example.

Type equation:

Preview:

Copy equation into message below

Close menu

Please click a symbol to insert it into the message box below:

Please enter the link here:

Optionally, you can enter text that should appear as linked text:

Copy link into message below

Close menu

Please enter or paste the URL to the image here (please only use links to jpg/jpeg, png and gif images):

Copy image into message below

Close menu

Type author name or keywords to filter the list of references in this group (you can add a new citation under Bibliography):

No existing citations in Discussion Group

Wikify editor is a simple editor for wiki-style mark-up. It was written by MDPI for Sciforum in 2014. The rendering of the mark-up is based on Wiky.php with some tweaks. Rendering of mathematical equations is done with MathJax. Please send us a message for support or for reporting bugs.

Close menu

Please declare any conflicts of interest you may have with this paper, financial or otherwise.

I do not have a conflict of interest

I would like to declare a conflict of interest

Display my name on the website I want to get recognition for my comment on Publons

[what’s this?]. Link your accounts here

Captcha

Renew

I accept the following conditions:

Comments must follow the standards of professional discourse and should focus on the scientific content of the article. Insulting or offensive language, personal attacks and off-topic remarks will not be permitted. Comments must be written in English. Preprints reserves the right to remove comments without notice. Readers who post comments are obliged to declare any competing interests, financial or otherwise.

Notify me about updates to this article or when a peer-reviewed version is published.

UniBioDicts: Unified access to Biological Dictionaries

Abstract

Supplementary and Associated Material

Subject Areas

Comments (0)