Record added: Oct. 28, 2020, 3:01 p.m.
Record updated: Feb. 4, 2021, 3:02 p.m. by The FAIRsharing Team.

Edits to 'https://fairsharing.org/FAIRsharing.6IBl8E' by 'The FAIRsharing Team' at 15:02, 04 Feb 2021 (approved):

	'dataProcesses' has been modified:
		Before:
			Data submission, data curation, http://discovery.informatics.uab.edu/PAGER/index.php/user_upload
			Basic search, data access, http://discovery.informatics.uab.edu/PAGER/index.php
			Advanced search, data access, http://discovery.informatics.uab.edu/PAGER/index.php/search/advanced
			Data download, data access, http://discovery.informatics.uab.edu/PAGER/index.php/pages/download
		After:
			Data submission, data curation, http://discovery.informatics.uab.edu/PAGER/index.php/user_upload
			Basic search, data access, http://discovery.informatics.uab.edu/PAGER/index.php
			Advanced search, data access, http://discovery.informatics.uab.edu/PAGER/index.php/search/advanced
			Data download, data release, http://discovery.informatics.uab.edu/PAGER/index.php/pages/download
		Added:
			Data download, data release, http://discovery.informatics.uab.edu/PAGER/index.php/pages/download
		Removed:
			Data download, data access, http://discovery.informatics.uab.edu/PAGER/index.php/pages/download

	'description' has been modified:
		Before: Pathway and Annotated-list Gene-signature Electronic Repository (PAGER), an online systems biology tool for constructing and visualizing gene and PAGs' networks from multiple PAG collections (PAG Data). 
		After: Pathway and Annotated-list Gene-signature Electronic Repository (PAGER) is an repository for pathways, annotated-lists, and gene signatures (PAGs) related to human network biology.

	'onto_domains' has been modified:
		Before:
			Pathway or network prediction
		After:
			Prediction and recognition
			network model
		Added:
			Prediction and recognition
			network model
		Removed:
			Pathway or network prediction

            

Edits to 'https://fairsharing.org/FAIRsharing.6IBl8E' by 'zongyue' at 21:07, 11 Nov 2020 (approved):

	'related_databases' has been modified:
		Before:
		After:
			GeneSigDB: a manually curated database and resource for analysis of gene expression signatures
			Pfam
			WikiPathways
			Gene Ontology Annotation Database
			Pharmacogenomics Knowledge Base
			Kyoto Encyclopedia of Genes and Genomes
			GTEx Portal
			Genome-Wide Association Studies Catalog
		Added:
			GeneSigDB: a manually curated database and resource for analysis of gene expression signatures
			Pfam
			WikiPathways
			Gene Ontology Annotation Database
			Pharmacogenomics Knowledge Base
			Kyoto Encyclopedia of Genes and Genomes
			GTEx Portal
			Genome-Wide Association Studies Catalog
		Removed:

	'standardsImplemented' has been modified:
		Before:
		After:
			Gene Ontology
		Added:
			Gene Ontology
		Removed:

	'accessPoints' has been modified:
		Before:
		After:
			REST|http://discovery.informatics.uab.edu/PAGER/index.php/geneset/pagerapi|PAGERCOV_ANALYSIS is to perform hypergeometric test and retrieve enriched PAGs associated to a list of genes
		Added:
			REST|http://discovery.informatics.uab.edu/PAGER/index.php/geneset/pagerapi|PAGERCOV_ANALYSIS is to perform hypergeometric test and retrieve enriched PAGs associated to a list of genes
		Removed:

            

Edits to 'https://fairsharing.org/FAIRsharing.6IBl8E' by 'The FAIRsharing Team' at 15:33, 04 Nov 2020 (approved):

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

	'onto_domains' has been modified:
		Before:
		After:
			Pathway or network prediction
		Added:
			Pathway or network prediction
		Removed:

            

Edits to 'https://fairsharing.org/FAIRsharing.6IBl8E' by 'The FAIRsharing Team' at 15:23, 04 Nov 2020 (approved):

	'supportLinks' has been modified:
		Before:
		After:
			help|http://discovery.informatics.uab.edu/PAGER/index.php/pages/help
		Added:
			help|http://discovery.informatics.uab.edu/PAGER/index.php/pages/help
		Removed:

	'name' has been modified:
		Before: An update to the pathway, annotated-list, and gene-signature electronic repository for Human Network Biology
		After: Pathway and Annotated-list Gene-signature Electronic Repository

	'dataProcesses' has been modified:
		Before:
		After:
			Data submission, data curation, http://discovery.informatics.uab.edu/PAGER/index.php/user_upload
			Basic search, data access, http://discovery.informatics.uab.edu/PAGER/index.php
			Advanced search, data access, http://discovery.informatics.uab.edu/PAGER/index.php/search/advanced
			Data download, data access, http://discovery.informatics.uab.edu/PAGER/index.php/pages/download
		Added:
			Data submission, data curation, http://discovery.informatics.uab.edu/PAGER/index.php/user_upload
			Basic search, data access, http://discovery.informatics.uab.edu/PAGER/index.php
			Advanced search, data access, http://discovery.informatics.uab.edu/PAGER/index.php/search/advanced
			Data download, data access, http://discovery.informatics.uab.edu/PAGER/index.php/pages/download
		Removed:

	'description' has been modified:
		Before: Integrative Gene-set, Network, and Pathway Analysis (GNPA) is a powerful data analysis approach developed to help interpret high-throughput omics data. In PAGER 1.0, we demonstrated that researchers can gain unbiased and reproducible biological insights with the introduction of PAGs (Pathways, Annotated-lists, and Gene-signatures) as the basic data representation elements. In PAGER 2.0, we improve the utility of integrative GNPA by significantly expanding the coverage of PAGs and PAG-to-PAG relationships in the database, defining a new metric to quantify PAG data qualities, and developing new software features to simplify online integrative GNPA. Specifically, we included 84,282 PAGs spanning 24 different data sources that cover human diseases, published gene-expression signatures, drug-gene, miRNA-gene interactions, pathways, and tissue-specific gene expressions. We introduced a new normalized Cohesion Coefficient (nCoCo) score to assess the biological relevance of genes inside a PAG, and RP-score to rank genes and assign gene-specific weights inside a PAG. The companion web interface contains numerous features to help users query and navigate the database content. The database content can be freely downloaded and is compatible with third-party Gene Set Enrichment Analysis (GSEA) tools. We expect PAGER 2.0 to become a major resource in integrative GNPA. PAGER 2.0 is available at http://discovery.informatics.uab.edu/PAGER/.
		After: Pathway and Annotated-list Gene-signature Electronic Repository (PAGER), an online systems biology tool for constructing and visualizing gene and PAGs' networks from multiple PAG collections (PAG Data). 

            

Edits to 'https://fairsharing.org/FAIRsharing.6IBl8E' by 'zongyue' at 15:09, 28 Oct 2020 (approved):

	'name' has been modified:
		Before: PAGER 2.0: An update to the pathway, annotated-list, and gene-signature electronic repository for Human Network Biology
		After: An update to the pathway, annotated-list, and gene-signature electronic repository for Human Network Biology

	'publications' has been modified:
		Before:
			PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology|Zongliang Yue1, Qi Zheng3, 1, Michael T. Neylon4, Minjae Yoo2, Jimin Shin2, Zhiying Zhao5, 1, Aik Choon Tan2, and Jake Y. Chen1* |Nucleic Acids Researcg|2017
		After:
			PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology|Zongliang Yue, Qi Zheng, Michael T. Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, and Jake Y. Chen|Nucleic Acids Researcg|2017
		Added:
			PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology|Zongliang Yue, Qi Zheng, Michael T. Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, and Jake Y. Chen|Nucleic Acids Researcg|2017
		Removed:
			PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology|Zongliang Yue1, Qi Zheng3, 1, Michael T. Neylon4, Minjae Yoo2, Jimin Shin2, Zhiying Zhao5, 1, Aik Choon Tan2, and Jake Y. Chen1* |Nucleic Acids Researcg|2017