regulondb-datamarts - RegulonDB-Datamarts 1.7.0

The following changes were applied:

New

• Added first version of evidencesDatamart

Update

• Changes applied for RegulonDB 14.0 version data
• Minor bugs fixed

- Python
Published by andresloal about 1 year ago

regulondb-datamarts - RegulonDB-Datamarts 1.6.5

The following changes were applied:

New

• Applied changes to be compatible with Ecocyc v28.5

Fix

• Multiple changes applied for downloadable files generation.
• Minor bugs fixed

- Python
Published by andresloal over 1 year ago

regulondb-datamarts - RegulonDB-Datamarts 1.6.0

The following changes were applied:

New

• Added sigma factor related to regulated operons of genes.regulation extraction
• Added bnumber column on regulatorSet and TFSet downloadable files extraction
• Applied changes to be compatible with Ecocyc v28.0

Fix

• The regulated genes in regulatory interactions now are displayed in order
• A release version were added to downloadable files
• Minor bugs fixed

- Python
Published by andresloal about 2 years ago

regulondb-datamarts - RegulonDB-Datamarts 1.5.0

The following changes were applied:

New

• Added an allPmids extraction for downloadable file (internal)
• Added extraction for Term Tree Collection

Fixed

• Fixed problems related to citations in all datamarts
• Fixed an error with forward promoter where distances were calculated incorrectly
• Other minor bugs fixed

Removed

• Removed unused properties

- Python
Published by andresloal about 2 years ago

regulondb-datamarts - RegulonDB-Datamarts 1.4.0

New

• Added extraction for evidence and additiveEvidences downloadable files

Fix

• Improved some functions to obtain data for extraction
• Errors related to previous versions and incorrect or missing data extraction were fixed
• Minor bugs fixed

- Python
Published by andresloal over 2 years ago

regulondb-datamarts - RegulonDB-Datamarts 1.3.0

The following changes were applied:

New

• Added extraction of the RegulonDB Downloadable files info

Update

• Updated all properties on extraction to format camelCase
• Corrected extraction on regulator due a change applied on activeConformations on transcriptionFactor items.

Fixed

• Minor bugs fixed

- Python
Published by andresloal almost 3 years ago

regulondb-datamarts - RegulonDB-Datamarts 1.2.0

The following changes were applied:

Fix

• All "id" properties were updated to "_id".
• Some property's name definitions were updated from snakecase to camelCase. The resume of the fields is here: > GeneDatamart >> gene.id -> gene.id >> gene.fragments.id -> gene.fragments.id >> gene.multifunTerms.id -> gene.multifunTerms.id >> products.id -> products.id >> products.motifs.id -> products.motifs.id >> regulation.operon.arrangement.[regulators, promoters, transcriptionUnit].id -> regulation.operon.arrangement.[regulators, promoters, transcriptionUnit].id >> organism.id -> organism.id

Operon

operon.id -> operon.id transcriptionUnit.id -> transcriptionUnit.id transcriptionUnit.firstGene.geneid -> transcriptionUnit.firstGene.id transcriptionUnit.firstGene.genename -> transcriptionUnit.firstGene.name transcriptionUnit.genes.id -> transcriptionUnit.genes.id transcriptionUnit.promoter.bindsSigmaFactor.id -> transcriptionUnit.promoter.bindsSigmaFactor.id organism.id -> organism.id

Regulon

transcriptionFactor.id -> transcriptionFactor.id transcriptionFactor.conformations.id -> transcriptionFactor.conformations.id transcriptionFactor.encodedFrom.genes.geneid -> transcriptionFactor.encodedFrom.genes.id transcriptionFactor.encodedFrom.genes.genename -> transcriptionFactor.encodedFrom.genes.name transcriptionFactor.encodedFrom.operon.operonid -> transcriptionFactor.encodedFrom.operon.id terms.multifun.id -> terms.multifun.id terms.multifun.genes.geneid -> terms.multifun.genes.id terms.multifun.genes.genename -> terms.multifun.genes.name terms.geneOntology.[cellularComponent, molecularFunction, biologicalProcess].id -> terms.geneOntology.[cellularComponent, molecularFunction, biologicalProcess].id terms.geneOntology.[cellularComponent, molecularFunction, biologicalProcess].genes.geneid -> terms.geneOntology.[cellularComponent, molecularFunction, biologicalProcess].genes.id terms.geneOntology.[cellularComponent, molecularFunction, biologicalProcess].genes.genename-> terms.geneOntology.[cellularComponent, molecularFunction, biologicalProcess].genes.name regulates.[genes, transcriptionFactors, transcriptionUnits, operons, sigmaFactors].id -> regulates.[genes, transcriptionFactors, transcriptionUnits, operons, sigmaFactors].id regulates.transcriptionFactors.genes.id -> regulates.transcriptionFactors.genes.id regulates.[transcriptionUnits, operons, sigmaFactors].firstGene.id -> regulates.[transcriptionUnits, operons, sigmaFactors].firstGene.id regulatoryInteractions.id Added regulatoryInteractions.regulatedGenes.id -> regulatoryInteractions.regulatedGenes.id regulatoryInteractions.regulatoryBindingSite.id -> regulatoryInteractions.regulatoryBindingSite.id organism.id -> organism.id

geneCoexpression

organism.id -> organism._id

Sigmulon

transcribedPromoters.operonid -> transcribedPromoters.operonId organism.id -> organism.id

SRNA

product.id -> product.id organism.id -> organism.id

dnaFeatures

relatedGenes.id -> relatedGenes.id organism.organimid -> organism.id organism.organismname -> organism._id

- Python
Published by andresloal over 3 years ago

regulondb-datamarts - RegulonDB-Datamarts 1.1.0

The following changes were applied:

New

• Added a list page extractor, this datamart is used for list objects for better use in RegulonDB-Browser

Updated

• Added and updated properties on multiple datamarts
• Improved extraction time in all datamarts extractor

Fix

• Minor changes applied

- Python
Published by andresloal over 3 years ago

regulondb-datamarts - RegulonDB-Datamarts 1.0.0

The following changes were applied:

Added

• Added clases for extraction of Gene Coexpression Datamart.
• Now the extraction of DNA Features collection can be maded for more biological entities (Regulatory Interaction, Transcription Factors Binding Sites, sRNAs, ppGpp and translationtfbinding_sites).
• Now the Regulatory Network Datamart can be fully extracted.
• Added a Datamarts Uploader Tool.

Updated

• Added more properties for extraction is some collections.
• Code improved in classes to reduce extraction time.

Fix

• Solved some mismatch properties in extraction of some collections.

- Python
Published by andresloal almost 4 years ago

regulondb-datamarts - RegulonDB-Datamarts 0.5.0

This version includes support for extraction of SRNA Datamart

Added

• Added classes for extraction of SRNA Datamart
• Added first version of classes for DnaFeatures Datamart for the following genetic elements: Gene, Promoters, Terminators

Fixed

• Solved a problem with notes that aren't formatted.
• Added _id property for transcriptionFactor object property on Regulon Service extraction

Additional Note

Json files obtained by this process are compatible with the version 0.5.1 of RegulonDB-GraphQL-API

- Python
Published by andresloal almost 5 years ago

regulondb-datamarts - RegulonDB-Datamarts 0.4.0

Release Notes

Added

• Functions for extraction of Sigmulon Datamart has been added

Updated

• Solved some bugs and added extraction for missing properties of Regulon and Operon Datamarts

Additional Note

Json files obtained by this process are compatible with the version 0.4.0 of RegulonDB-GraphQL-API

- Python
Published by andresloal about 5 years ago