iPathwayGuide Release Notes
On January 12, 2018, Advaita released a major updates to its platform, with improvements to iPathwayGuide, iVariantGuide, and iBioguide.
The Advaita Knowledgebase was updated to version 1711 and now includes:
- 3 organisms: homo sapiens, mus musculus, rattus norvegicus
- 213,390 Genes
- 1,933 Diseases
- 44,976 GO terms
- 4,791 Drugs
- 955 Pathways
- 5,710 miRNAs
- 3,161,730 References
For a complete list of databases and versions, please see report information within each application.
- iVariantGuide: API Client now accepts multi-sample analyses
- Improvements to account registration page to ensure proper organization affiliation.
- iPathwayGuide: Improvements to parsing of CuffDiff-formatted files to maintain association of phenotype labels. Fold changes and p-value parsing remains untouched.
With Advaita’s latest update to its applications and knowledge base, Advaita updated its API for iVariantGuide and iPathwayGuide.
An API or (Application Program Interface) is a set of routines, protocols, and tools for building software applications. An API specifies how software components should interact. Advaita’s API is designed.
On February 27, 2017, Advaita released a major updates to its platform. These are the release notes.
IMPROVEMENTS TO: iPathwayGuide, iVariantGuide, iBioguide, and the Advaita Knowledge Base
- Changes to AWS services in preparation for HIPAA compliance
- Updated knowledge base to version Advaita KB v1702, which includes the following data sources and versions:
|Database||Version||iPG Annotations||iVG Annotations|
|KEGG||Release 81.0+/01-20, Jan 17||Pathways, Diseases, Drugs||Pathways|
|Gene Ontology||2016-Sep26||GO Terms||GO Terms|
|Targetscan||Targetscan v7.1||miRNA Target Genes||miRNA Target Genes|
|MIRBASE||MIRBASE v21,06/14||miRNA Sequences|
|dbSNP (incl 1k genomes)||Build 149||Minor Allele freq.|
|RefSeq||Release 71 July 2016||Impacted Transcripts|
|ClinVar||Dec 1, 2016||Clinical Significance|
IMPROVEMENTS TO iPATHWAYGUIDE
- NEW FEATURE! Onboarding carousel with top user benefits
- NEW FEATURE! API (Premium feature)
- Bug fix: genes selected in Genes Table on Pathways page are now highlighted on pathway map
IMPROVEMENTS TO iVARIANTGUIDE
- Improved error messaging for sample upload & report creation
- NEW FEATURE! Versioning: each report now shows which version of the Advaita Knowledgebase was used to annotate the sample. Outdated reports may be updated when viewing Report Info: either on the Reports page or from within the report itself. As is true for other Advaita applications, only the report owner may update it.
IMPROVEMENTS TO iBIOGUIDE
- Updated to use AKB v1702
The following components were added or addressed in this release.
- Extensive databases updates including:
- KEGG pathways, drugs, and diseases
- NCBI genes
- TargetScan miRNAs
- Gene Ontologies
- PubMed references
- New EdgeR import format support
- Improvements to several of the exported images
- Improvements to meta analysis to preserve order of comparisons
- Several bug fixes
- Changes to support additional AWS features
- Enhancements to security
The following components were added:
- Support for Sciex SWATH 2.0 Proteomics Expression data
- “Trash” bin on user dashboard
- Pathway and ontology images are now locked for scrolling. They can be unlocked in the on-screen menu.
- In the pathway images, individual genes can now be selected if you hover over the node in the image.
- Coherent cascades now have arrow heads so you can see directionality of the cascade.
- The gene table in the pathway detail page is more refined. Easier to filter.
- Bar chart of DE genes for pathways is now presented below the pathway image.
- Meta-analysis has a new view called “Rank layout” that lets you see how genes, GO terms, pathways, etc, rank compared to each other. (accessible from the
- lower right corner of the Venn).
- Several other improvements on the back-end and a few bug fixes.
Knowledge Base Updates:
- Genes – 195,222 (increase of 23,106)
- Pathways – 871 (increase of 12)
- micro RNAs – 8,837 (increase of 5,268)
- GO Terms – 39,907 (increase of 1,880)
- Drugs – 4,389 (increase of 229)
- Diseases – 1,411 (increase of 12)
- SNPs – 92,169,423 (increase of 32,120,131)
- References – 3,010,588 (increase of 51,977)
- Support for nSolver data from NanoString Technologies
- QC and Normalization metrics for Affymetrix CEL files
- Stem-loop information for miRNAs
- Printable report summary with detailed methods and references
- “Line-up” comparative ranking chart in meta analysis