BIOchemical PathwaY DataBase

Abbreviation:BIOPYDB

General Information

BIOPYDB is a manually-curated database of human cell specific biochemical pathway data. The information within BIOPYDB is primarily extracted from published scientific literature and a selection of databases. The reconstructed pathways contain information about proteins, protein complexes, inorganic molecules, mutated and onco-proteins of signalling, disease and immunological pathways. Every molecule and interaction listed in the database contains at least one reference in a peer reviewed journal.

Homepage http://biopydb.ncl.res.in/biopydb/index.php

Countries that developed this resource India

Created in 2017

Taxonomic range

Homo sapiens

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: BIOPYDB; BIOchemical PathwaY DataBase; DOI: https://doi.org/10.25504/FAIRsharing.ANR6qz; Last edited: March 19, 2021, 1:20 p.m.; Last accessed: May 12 2021 9:49 p.m.

Publication for citation BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. Chowdhury S,Sinha N,Ganguli P,Bhowmick R,Singh V,Nandi S,Sarkar RR; J Integr Bioinform ; 2018; 10.1515/jib-2017-0072;

This record is maintained by ramrup

Record added: Sept. 9, 2019, 2:25 p.m.
Record updated: Feb. 24, 2021, 10:48 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.ANR6qz' by 'The FAIRsharing Team' at 10:48, 24 Feb 2021 (approved):

	'grants' has been modified:
		Before:
			10.13039/501100001412 (BSC0114)
			10.13039/501100001412 (BSC0121)
			Funder Id: 10.13039/501100001843, No. EMR/2016/000516
		After:
			10.13039/501100001412 (BSC0114)
			10.13039/501100001412 (BSC0121)
			Funder Id: 10.13039/501100001843 - No. EMR/2016/000516
		Added:
			Funder Id: 10.13039/501100001843 - No. EMR/2016/000516
		Removed:
			Funder Id: 10.13039/501100001843, No. EMR/2016/000516

Edits to 'https://fairsharing.org/FAIRsharing.ANR6qz' by 'The FAIRsharing Team' at 13:43, 04 Feb 2021 (approved):

	'onto_domains' has been modified:
		Before:
			Biocuration
			Pathway or network prediction
			Protein-Protein Interaction
			curated information
			disease
		After:
			Biocuration
			Prediction and recognition
			Protein-Protein Interaction
			curated information
			disease
			mutation
			protein-containing complex
			signaling
		Added:
			Prediction and recognition
			mutation
			protein-containing complex
			signaling
		Removed:
			Pathway or network prediction

Edits to 'https://fairsharing.org/FAIRsharing.ANR6qz' by 'The FAIRsharing Team' at 09:39, 31 Jan 2020 (approved):

	'organizations' has been modified:
		Before:
			Chemical Engineering and Processing Development (CEPD), CSIR-National Chemical Laboratory, Pune, India|http://www.ncl-india.org/files/Research/Organisation/GroupDetails.aspx?Category=3&Id=25&menuid=ql2&childmenustripid=divSubQL2|Maintains
			Council of Scientific and Industrial Research (CSIR), New Delhi, India|https://www.csir.res.in|Funds
		After:
			Council of Scientific and Industrial Research (CSIR), New Delhi, India|https://www.csir.res.in|Funds
			Chemical Engineering and Processing Development (CEPD), CSIR-National Chemical Laboratory, Pune, India|http://www.ncl-india.org/files/Research/Organisation/GroupDetails.aspx?Category=3&Id=25&menuid=ql2&childmenustripid=divSubQL2|Maintains
			Council of Scientific and Industrial Research, XII Five Year Plan Project GENESIS |https://www.csir.res.in/|Funds
			Council of Scientific and Industrial Research, XII Five Year Plan Project HOPE |https://www.csir.res.in/|Funds
			SERB, Ministry of Science and Technology, Government of India|http://www.serb.gov.in/home.php|Funds
		Added:
			Council of Scientific and Industrial Research, XII Five Year Plan Project GENESIS |https://www.csir.res.in/|Funds
			Council of Scientific and Industrial Research, XII Five Year Plan Project HOPE |https://www.csir.res.in/|Funds
			SERB, Ministry of Science and Technology, Government of India|http://www.serb.gov.in/home.php|Funds
		Removed:

	'supportLinks' has been modified:
		Before:
			contact form|http://biopydb.ncl.res.in/biopydb/contactform.html
			online documentation|http://biopydb.ncl.res.in/biopydb/FAQ.html
		After:
			FAQ|http://biopydb.ncl.res.in/biopydb/FAQ.html
			contact form|http://biopydb.ncl.res.in/biopydb/contactform.html
			email|biopydb@gmail.com
		Added:
			FAQ|http://biopydb.ncl.res.in/biopydb/FAQ.html
			email|biopydb@gmail.com
		Removed:
			online documentation|http://biopydb.ncl.res.in/biopydb/FAQ.html

	'contactORCID' has been modified:
		Before: 
		After: 0000-0001-7115-163X

	'onto_disciplines' has been modified:
		Before:
			Biochemistry
		After:
			Biochemistry
			Life Science
			Proteomics
		Added:
			Life Science
			Proteomics
		Removed:

	'onto_domains' has been modified:
		Before:
			Biocuration
			Protein-Protein Interaction
			curated information
			disease
		After:
			Biocuration
			Pathway or network prediction
			Protein-Protein Interaction
			curated information
			disease
		Added:
			Pathway or network prediction
		Removed:

	'contact' has been modified:
		Before: 
		After: Ram Rup Sarkar

	'contactEmail' has been modified:
		Before: biopydb@ncl.res.in
		After: rr.sarkar@ncl.res.in

	'grants' has been modified:
		Before:
		After:
			10.13039/501100001412 (BSC0114)
			10.13039/501100001412 (BSC0121)
			Funder Id: 10.13039/501100001843, No. EMR/2016/000516
		Added:
			10.13039/501100001412 (BSC0114)
			10.13039/501100001412 (BSC0121)
			Funder Id: 10.13039/501100001843, No. EMR/2016/000516
		Removed:

	'dataProcesses' has been modified:
		Before:
			Browse Pathways
			Pathway Visualization
			Network Analysis
			Find a Disease
			Download
			Find an Interaction
			Upload Pathway
		After:
			Browse Pathways
			Pathway Visualization
			Network Analysis
			Find a Disease
			Download
			Find an Interaction
			Upload Pathway
			Advanced search
		Added:
			Advanced search
		Removed:

Support

General

FAQ	FAQ
contact form	Feedback Form
support email	General contact

Additional Information

Contact

Ram Rup Sarkar ORCID

Tools

Dynamic Analysis using ODEs	http://biopydb.ncl.res.in/biopydb/ode_analysis.php
Logical Analysis	http://biopydb.ncl.res.in/boolean_app/index.php

Access / Retrieve Data

Conditions of Use

Data Release

Download

http://biopydb.ncl.res.in/biopydb/HomePathwayList.php

Data Curation

Upload Pathway

http://biopydb.ncl.res.in/insert_upload/browse_pathway_tab.php

Data Access

Browse Pathways	http://biopydb.ncl.res.in/biopydb/browse_pathway_tab.html
Pathway Visualization	http://biopydb.ncl.res.in/biopydb/pathway_drawing.php
Network Analysis	http://biopydb.ncl.res.in/biopydb/graph_drawing.php
Find a Disease	http://biopydb.ncl.res.in/biopydb/Find_Disease.php
Find an Interaction	http://biopydb.ncl.res.in/biopydb/Find_Interaction.php
Advanced search	http://biopydb.ncl.res.in/biopydb/AdvanceSearchPHP.php

REST Web Services

BIOPYDB RESTful API

http://biopydb.ncl.res.in/biopydb/HomePathwayList.php

Publications

BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform.

Chowdhury S,Sinha N,Ganguli P,Bhowmick R,Singh V,Nandi S,Sarkar RR
J Integr Bioinform 2018

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Pathway Ontology

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by ramrup

Funds

Council of Scientific and Industrial Research (CSIR), New Delhi, India (Government body)
Council of Scientific and Industrial Research, XII Five Year Plan Project, GENESIS (Government body)
Council of Scientific and Industrial Research, XII Five Year Plan Project, HOPE (Government body)
SERB, Ministry of Science and Technology, Government of India (Government body)

Maintains

Chemical Engineering and Processing Development (CEPD), CSIR-National Chemical Laboratory, Pune, India (Research institute) Lead

Grant Number(s)

10.13039/501100001412 (BSC0114) (Council of Scientific and Industrial Research, XII Five Year Plan Project, HOPE)
10.13039/501100001412 (BSC0121) (Council of Scientific and Industrial Research, XII Five Year Plan Project, GENESIS)
Funder Id: 10.13039/501100001843 - No. EMR/2016/000516 (SERB, Ministry of Science and Technology, Government of India)

BIOchemical PathwaY DataBase

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