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Synapse

Recommended

General Information

Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. It provides infrastructure and hosting for datasets.

Homepage https://www.synapse.org/

Countries that developed this resource United States

Created in 2010

Taxonomic range

All

Knowledge Domains

Subjects

User-defined Tags

Data sharing

In the following recommendations:

How to cite this record FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Jan. 8, 2019, 1:23 p.m.; Last accessed: Jun 02 2020 3:08 p.m.

This record is maintained by SageSynapse

Record added: Aug. 2, 2016, 2:56 p.m.
Record updated: Dec. 18, 2018, 10:46 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.dnxzmk' by 'The FAIRsharing Team' at 10:46, 18 Dec 2018 (approved):

	'organizations' has been modified:
		Before:
			NIH LINCS Program, USA|http://www.lincsproject.org|Funds
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			Oregon Health & Science University, USA|http://www.ohsu.edu/xd/education/library/about/departments/ontology-development.cfm|Maintains
		After:
			Sage Bionetworks|http://sagebionetworks.org/|Maintains
		Added:
			Sage Bionetworks|http://sagebionetworks.org/|Maintains
		Removed:
			NIH LINCS Program, USA|http://www.lincsproject.org|Funds
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			Oregon Health & Science University, USA|http://www.ohsu.edu/xd/education/library/about/departments/ontology-development.cfm|Maintains

	'standardsImplemented' has been modified:
		Before:
			UBER anatomy ONtology
			Chemical Entities of Biological Interest
			Investigation Study Assay Tabular
			Systematized Nomenclature of Medicine-Clinical Terms
			Open Microscopy Environment eXtensible Markup Language
			NCBI Taxonomy
			Medical Subject Headings
		After:
		Added:
		Removed:
			UBER anatomy ONtology
			Chemical Entities of Biological Interest
			Investigation Study Assay Tabular
			Systematized Nomenclature of Medicine-Clinical Terms
			Open Microscopy Environment eXtensible Markup Language
			NCBI Taxonomy
			Medical Subject Headings

	'accessPoints' has been modified:
		Before:
		After:
			REST|https://repo-prod.prod.sagebase.org/repo/v1|Synapse REST APIs
		Added:
			REST|https://repo-prod.prod.sagebase.org/repo/v1|Synapse REST APIs
		Removed:

	'supportLinks' has been modified:
		Before:
		After:
			email|synapseinfo@sagebionetworks.org
			help|https://docs.synapse.org/
			online documentation|https://docs.synapse.org/articles/governance.html
			online documentation|https://docs.synapse.org/articles/accounts_certified_users_and_profile_validation.html
			online documentation|https://www.synapse.org/#!StandaloneWiki:ResearchCommunities
			online documentation|https://www.synapse.org/#!StandaloneWiki:OpenResearchProjects
		Added:
			email|synapseinfo@sagebionetworks.org
			help|https://docs.synapse.org/
			online documentation|https://docs.synapse.org/articles/governance.html
			online documentation|https://docs.synapse.org/articles/accounts_certified_users_and_profile_validation.html
			online documentation|https://www.synapse.org/#!StandaloneWiki:ResearchCommunities
			online documentation|https://www.synapse.org/#!StandaloneWiki:OpenResearchProjects
		Removed:

	'name' has been modified:
		Before: Microenvironment Perturbagen LINCS Center image server
		After: Synapse

	'licences' has been modified:
		Before:
			No restrictions||Data
		After:
			Synapse Apache 2.0|https://github.com/Sage-Bionetworks/Synapse-Repository-Services/blob/develop/LICENSE|Software
			Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data
		Added:
			Synapse Apache 2.0|https://github.com/Sage-Bionetworks/Synapse-Repository-Services/blob/develop/LICENSE|Software
			Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data
		Removed:
			No restrictions||Data

	'tools' has been modified:
		Before:
		After:
			Synapse R Client||https://sage-bionetworks.github.io/ran/
			Synapse Python Client||https://pypi.org/project/synapseclient/
			Synapse Command-Line Client||http://docs.synapse.org/python/build/html/CommandLineClient.html
			Synapse Java Client||https://github.com/Sage-Bionetworks/Synapse-Repository-Services/blob/develop/client/synapseJavaClient/src/main/java/org/sagebionetworks/client/SynapseClient.java
		Added:
			Synapse R Client||https://sage-bionetworks.github.io/ran/
			Synapse Python Client||https://pypi.org/project/synapseclient/
			Synapse Command-Line Client||http://docs.synapse.org/python/build/html/CommandLineClient.html
			Synapse Java Client||https://github.com/Sage-Bionetworks/Synapse-Repository-Services/blob/develop/client/synapseJavaClient/src/main/java/org/sagebionetworks/client/SynapseClient.java
		Removed:

	'yearOfCreation' has been modified:
		Before: 2016
		After: 2010

	'onto_disciplines' has been modified:
		Before:
			Life Sciences
		After:
			Biomedical Science
			Data Integration and Warehousing
			Data Management
		Added:
			Biomedical Science
			Data Integration and Warehousing
			Data Management
		Removed:
			Life Sciences

	'onto_domains' has been modified:
		Before:
			Biological imaging
			imaging technique
			transcript
		After:
			Experiment report
			data storage
		Added:
			Experiment report
			data storage
		Removed:
			Biological imaging
			imaging technique
			transcript

	'contact' has been modified:
		Before: Damir Sudar
		After: Meredith Slota

	'contactEmail' has been modified:
		Before: sudard@ohsu.edu
		After: meredith.slota@sagebionetworks.org

	'user_defined_tags' has been modified:
		Before:
		After:
			Data sharing
		Added:
			Data sharing
		Removed:

	'grants' has been modified:
		Before:
			U54 HG008100
		After:
		Added:
		Removed:
			U54 HG008100

	'publications' has been modified:
		Before:
		After:
			Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas.|Omberg L,Ellrott K,Yuan Y,Kandoth C,Wong C,Kellen MR,Friend SH,Stuart J,Liang H,Margolin AA|Nat Genet|2013
		Added:
			Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas.|Omberg L,Ellrott K,Yuan Y,Kandoth C,Wong C,Kellen MR,Friend SH,Stuart J,Liang H,Margolin AA|Nat Genet|2013
		Removed:

	'contactORCID' has been modified:
		Before: 
		After:  https://orcid.org/0000-0001-8492-6705

	'related_databases' has been modified:
		Before:
			Ensembl
			UniProt Knowledgebase
			Library of Integrated Network-Based Cellular Signatures Data Portal
			Synapse
		After:
		Added:
		Removed:
			Ensembl
			UniProt Knowledgebase
			Library of Integrated Network-Based Cellular Signatures Data Portal
			Synapse

	'shortname' has been modified:
		Before: MEP LINCS
		After: Synapse

	'taxonomies' has been modified:
		Before:
			Homo sapiens
		After:
			All
		Added:
			All
		Removed:
			Homo sapiens

	'homepage' has been modified:
		Before: https://www.synapse.org/#!Synapse:syn2862345/wiki/72486
		After: https://www.synapse.org/

	'description' has been modified:
		Before: The MEP LINCS project contributes to the development
of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) program by developing a dataset and computational strategy to elucidate how microenvironment (ME) signals affect cell intrinsic
intracellular transcriptional- and protein-defined molecular networks to generate experimentally observable cellular phenotypes measured by high-content imaging.
		After: Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. It provides infrastructure and hosting for datasets.

Edits to 'https://fairsharing.org/FAIRsharing.dnxzmk' by 'The FAIRsharing Team' at 12:06, 10 Jan 2018 (approved):

	'name' has been modified:
		Before: Microenvironment Perturbagen (MEP) LINCS Center image server
		After: Microenvironment Perturbagen LINCS Center image server

In Collections

Euro-BioImaging

Support

General

support email	Synapse Information Email
help	Synapse Documentation
online documentation	Synapse Commons Governance Overview
online documentation	About Accounts, Certification and Profil ...
online documentation	Synapse Research Communities
online documentation	Synapse Open Research Projects

Additional Information

Contact

Meredith Slota ORCID

Tools

Synapse R Client	https://sage-bionetworks.github.io/ran/
Synapse Python Client	https://pypi.org/project/synapseclient/
Synapse Command-Line Client	http://docs.synapse.org/python/build/html/CommandLineClient.html
Synapse Java Client	https://github.com/Sage-Bionetworks/Synapse-Repository-Services/blob/d ...

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution 4.0 International (CC BY 4.0)

Applies to: Database software

Synapse Apache 2.0

REST Web Services

Synapse REST APIs

https://repo-prod.prod.sagebase.org/repo/v1

Publications

Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas.

Omberg L,Ellrott K,Yuan Y,Kandoth C,Wong C,Kellen MR,Friend SH,Stuart J,Liang H,Margolin AA
Nat Genet 2013

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

No related databases defined

Implementing Policies

Credit

Record Maintainer

This record is maintained by SageSynapse

Maintains

Sage Bionetworks (Research institute) Lead

Synapse

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