Table 1 Overview of Databases and tools used within the workflow
From: Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations
Database/tool [reference] | Description | Workflow Step |
|---|---|---|
ChEBI [17] | Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds | 1–3, 5–7 |
Wikidata [18] | Wikidata is a free and open knowledge base that can be read and edited by both humans and machines | 1 |
UHPLC-MS/MS [19] | Ultra High-Performance Liquid Chromatography-Tandem Mass Spectrometer is a chemical technique combining the physical separation capabilities of liquid chromatography with the mass analysis capabilities of mass spectrometry | 1 |
PathVisio [20] | PathVisio is a free open-source pathway analysis and drawing software that allows drawing, editing, and analyzing biological pathways | 2 |
UniProt [21] | UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects | 2 |
Rhea [22] | Rhea is an expert-curated knowledge base of chemical and transport reactions of biological interest—and the standard for enzyme and transporter annotation in UniProtKB | 2 |
OMIM [23] | Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available | 2 |
WikiPathways [24] | WikiPathways is a database of biological pathways maintained by and for the scientific community | 2, 4, 6, 7 |
WikiPathways SPARQL Endpoint [25] | The semantic web format of the WikiPathways database, using the Resource Description Framework (RDF) as data format which can be queried through the SPARQL-query language | 2, 4, 6, 7 |
HGNC (gene ID) [26] | The HGNC is a resource for approved human gene nomenclature | 4 |
HMDB [27] | The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body | 4, 5 |
Cytoscape (REST API) [28] | Cytoscape is an open-source software platform for visualizing complex networks and integrating these with any type of attribute data. cyREST is a language-agnostic, programmer-friendly RESTful API module for Cytoscape, allowing for programmatic access to Cytoscape features | 7 |
GitHub (github.com) | GitHub is a web-based hosting service for version control using git | 1–8 |