PANTHER Pathway: an ontology-based pathway database coupled with data analysis tools

By Huaiyu Mi, Paul D. Thomas. Methods in molecular biology, 2009

712 citations recorded by the source corpus.

The availability of whole genome sequences from various model organisms and increasing experimental data and literatures stimulated the evolution of a systems approach for biological research. The development of computational tools and algorithms to study biological pathway networks has made great progress in helping analyze research data. Pathway databases become an integral part of such an approach. This chapter first discusses how biological knowledge is represented, particularly the importance of ontologies or standards in systems biology research. Next, we use PANTHER Pathway as an example to illustrate how ontologies and standards play a role in data modeling, data entry, and data display. Last, we describe the usage of such systems. We also describe the computational tools that utilize PANTHER pathway information to analyze gene expression experimental data.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7cd2a50b1c3b6288104221aad5fd75235147d570

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Citations in the corpus

Large-scale gene function analysis with PANTHER Classification System (2013, methodology): “In 2005, we began providing annotations of biochemical pathways, which can be viewed via the new PANTHER pathway applet 6,7 .”
PANTHER: Making genome‐scale phylogenetics accessible to all (2021, positive): “14 We joined in the effort to create the BioPAX standard for sharing annotated pathway information, 15 and have made PANTHER Pathways available in this format since that time.”
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API (2020, methodology): “This service supports various annotation data sets: Complete GO (three aspects, listed above), PANTHER GO-slim (three aspects), PANTHER Protein Class, PANTHER Pathway, and Reactome Pathways.”
MicrobesOnline: an integrated portal for comparative and functional genomics (2009, methodology): “FastBLAST and FastHMM (13) are used to search against the TIGRFAM (14), Superfamily (15), SMART (16), Pfam (17), Panther (18), PirSF (19), Gene3D (20), COG (21), PDB (22) and UniProt (23) databases.”
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements (2016, background): “In addition to GO terms, PANTHER also provides curated associations of genes to biological pathways from the PANTHER Pathway resource (3).”
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools (2018, background): “In addition to the GO, functional classification in PANTHER also includes biological pathways, both PANTHER pathways (15) and Reactome pathways (16).”
PANTHER version 10: expanded protein families and functions, and analysis tools (2015, methodology): “PANTHER Pathway Signaling and metabolic pathways manually curated by experts (16) PANTHER GO-slim Molecular Function Phylogenetically inferred annotations, to a reduced set of GO molecular function terms (GO-slim).”
Overview of BioNLP Shared Task 2013 (2013, methodology): “The PC task corpus was newly annotated for the task and consists of 525 PubMed abstracts, chosen for the relevance to specific pathway reactions selected from SBML models registered in BioModels and PANTHER DB repositories (Mi and Thomas, 2009).”
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees (2012, methodology): “The pathway role annotations were performed by expert curators, based on experimental evidence reported in the literature (26), and are focused”