graphql-api - RegulonDB-WS-API 1.15.5

The following changes were applied:

New

• Added a service to list all strategies of the datasets
• Added a first version of evidences service

Updated

• Removed datasetType on collection level
• Modified growth conditions object to object array
• Modified aerationSpeed property name on Growth Conditions due an error to agitationSpeed
• Added new properties of the experiment on Growth Conditions

Fix

• Minor bugs fixed

- JavaScript
Published by andresloal 12 months ago

graphql-api - RegulonDB-WS-API 1.15.0

The following changes were applied:

New

• Updated model for RegulonDB HT dataset service, this change is able to deal with the upcoming update for RegulonDB-HT data from different sources.
• Added a first version of new service for Growth Conditions

Update

• Changed mco service name to ontologyTree

Fix

• Some property's name changed due standard.
• Bugs fixed

- JavaScript
Published by andresloal about 1 year ago

graphql-api - RegulonDB-WS-API 1.14.2

This version contains the following changes:

New

Added summary property to Gensor Unit Service model

- JavaScript
Published by andresloal over 1 year ago

graphql-api - RegulonDB-WS-API 1.14.1

The following changes were applied:

New

• Restructured object for regulons on statistics

- JavaScript
Published by andresloal almost 2 years ago

graphql-api - RegulonDB-WS-API 1.14.0

The following changes were applied:

Fix

• Solved a problem when limit is added by the user and adds pagination data to query.
• Minor bugs fixed

Update

• Updated model on Gene in regulation adding new properties
• Removed the node version required to install
• Updated used libraries to latest version

- JavaScript
Published by andresloal almost 2 years ago

graphql-api - RegulonDB-WS-API 1.13.0

The following changes were applied:

New

• Added citations to gene terms
• Added positions to regulated genes of regulatory interactions.

- JavaScript
Published by andresloal almost 2 years ago

graphql-api - RegulonDB-WS-API 1.12.3

The following changes were applied:

New

• Added confidenceLevel property on regulatorBindingSite of Operon

Fixed

• Fixed type of organism property of Gene
• Updated test cases

- JavaScript
Published by andresloal about 2 years ago

graphql-api - RegulonDB-WS-API 1.12.2

The Following changes were applied:

New

• Added a service to retrieve all superclasses of a term

- JavaScript
Published by andresloal about 2 years ago

graphql-api - RegulonDB-WS-API 1.12.1

The Following changes were applied:

New

• Added a service getTermBy on termTree service
• Added a service to get all terms

Update

• Added some properties on Downloadable Files

Fixed

• Solved an compatibility issue related to mongoose
• Removed some innecesary blank spaces
• Minor bugs fixed

- JavaScript
Published by andresloal about 2 years ago

graphql-api - RegulonDB-WS-API 1.12.0

The following changes were applied:

New

• A first version of MCO Term Tree Service were added to listed functional services
• Minor bugs fixed

- JavaScript
Published by andresloal about 2 years ago

graphql-api - RegulonDB-WS-API 1.11.3

The following changes were applied:

Updated

• Changed type of effector property to object array

New

• Added conformation class property (active or inactive)
• Added rdbVersion property to downloadableFiles schema

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.11.2

The following changes were applied:

New

• Added a new service on downloable files to list all filenames

Fix

• Minor bugs fixed

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.11.1

Update

• This version adds capability to search in abbreviatedName in the following services: Regulon, Sigmulon. Gene (products.abbreviatedName)
• Added citations properties to dnaFeatures service

Fix

• Minor bugs fixed

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.11.0

New

• The following changes were applied in the following services: > Gene Service >>products.abbreviatedName was added

Operon Service

transcriptionUnits.promoter.bindsSigmaFactor.abbreviatedName was added

Regulon Service

regulator.abbreviatedName was added regulator.products.abbreviatedName was added regulator.encodedFrom was updated to regulator.encodedBy

Sigmulon Service

sigmaFactor.abbreviatedName was added

Fix

• An error related to regulated genes in Regulon Service was solved
• An error that doesn't show _id of terms in gensorUnit.geneOntology was solved

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.10.1

Fix

• Removed field to search on sigmulon service

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.10.0

The Following changes were applied:

New

• Added services for downloadable files datamart

Update

• Added strand to transcribedPromoters in Sigmulon datamart
• Added sourceReferenceGenome property in dataset on HT datasets datamart

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.9.3

New

• Added geneOntologyTerms to sigmulonGenes object
• Added TSS Position to transcribed promoters object

Fix

• Minor bugs fixed

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.9.2

The following changes were applies:

Update

• Added properties in statistics object of dbInfo collection making relevant the quantity of each object that have evidences, publications and no confidence level.

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.9.1

The following changes were applied:

Update

• On Operon collection some fields names and types were changed:

  • In all levels, regulatoryBindingSite.RegulatoryInteraction.centerPosition to regulatoryBindingSite.RegulatoryInteraction.relativeCenterPosition
  • In all levels, regulatoryBindingSite.RegulatoryInteraction.regulatorySite.absoluteCenterPosition to regulatoryBindingSite.RegulatoryInteraction.regulatorySite.centerEndPosition
  • In all levels, regulatoryBindingSites.mechanism is now a String Array

• On Regulon collection the notes of the regulator conformations when this is a transcription factor now includes their note and a effector object if the conformation is a complex.

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.9.0

The following changes were applied:

Update

• Added route and regulondbPMID to databaseInfo collection
• Added additiveEvidences object on regulatorBindingSites in transcriptionUnit, transcriptionUnit.promoter and transcriptionUnit.genes on operon collection
• Added totalOfReactions on gensorUnit collection

Fix

• Minor bugs fixed

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.8.1

Fix

• Added a sort value for dbInfo service

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.8.0

The following changes were applied:

New

• Added a new service to get all properties on datamart, this new service is getProperties

Update

• transcriptionFactor property was renamed to regulator
• regulator on regulatoryInteraction was renamed to activeConformation
• genomePosition on regulator.encodedFrom.genes were updated to leftEndPosition and rightEndPosition.

Fix

• Minor bugs solved

- JavaScript
Published by andresloal over 2 years ago

graphql-api - RegulonDB-WS-API 1.7.2

The following changes were applied:

Fix

• Solved Bugs

- JavaScript
Published by andresloal almost 3 years ago

graphql-api - RegulonDB-WS-API 1.7.1

The following changes were applied:

Update

• Default limit value were removed from all services

- JavaScript
Published by andresloal almost 3 years ago

graphql-api - RegulonDB-WS-API 1.7.0

The following changes were applied:

Update

• The changes on dbInfo model were applied to model and schema of service.

- JavaScript
Published by andresloal almost 3 years ago

graphql-api - RegulonDB-WS-API 1.6.2

The following changes were applied:

Fixed

• genomePosition on product.gene were split into leftEndPosition and rightEndPosition

- JavaScript
Published by andresloal almost 3 years ago

graphql-api - RegulonDB-WS-API 1.6.1

The following changes were applied:

Fix

• Some examples on schemas were updated and solved from previous changes applied to models.
• A mismatch property name on Gensor Unit service was updated correctly.

- JavaScript
Published by andresloal almost 3 years ago

graphql-api - RegulonDB-WS-API 1.6.0

The following changes were applied:

New

• Added a new previous level for HT Datasets services in order to retrieve its metadata.

Docs

• Updated test cases files to this new datamart model.

Update

• All "id" properties were updated to "_id".
• Some property's name definitions were updated from snake_case to camelCase.
• The resume of the fields is here: > Citations In All Collections >> publications.id -> publications.id >> evidences.id -> evidences.id

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

- JavaScript
Published by andresloal almost 3 years ago

graphql-api - RegulonDB-WS-API 1.5.3

The following changes were applied:

Fix

• Solved a bug related to latest property added in overviews service

- JavaScript
Published by andresloal about 3 years ago

graphql-api - RegulonDB-Ws-API 1.5.2

The following changes were applied:

Updated

• Added a type property on overview service in data.objectsRelated

- JavaScript
Published by andresloal about 3 years ago

graphql-api - RegulonDB-WS-API 1.5.1

The following changes were applied:

Updated

• Added capability of retrieve srna objets for list

Fix

• Minor bugs solved

- JavaScript
Published by andresloal about 3 years ago

graphql-api - RegulonDB-WS-API 1.5.0

The following changes were applied:

New

• A service to list a resume of docs in all datamarts were added as listPage Service, the query is named getObjectList and retrives a list of docs of specific datamart in alphabetical order with the necessary info for list

Update

• Some types were dupplicated in most datamarts, this dupplicated were optimized to few types for definition in schemas to improve code maintenance

- JavaScript
Published by andresloal about 3 years ago

graphql-api - RegulonDB-WS-API 1.4.0

The following changes were applied:

New

• Added a first version of additive Evidences in Regulon and Operon services.

Update

• Added new properties on Regulon Service that previously versions doesn't contains.

- JavaScript
Published by andresloal about 3 years ago

graphql-api - RegulonDB-WS-API 1.3.0

The following changes were applied:

New

• Merge with RegulonDBHT API Services
• Added services to insert and query the previously used queries strings.

Updated

• Added bnumber to gene service to be queried by text search

Fix

• Solved a bug related to Gensor Unite Services

- JavaScript
Published by andresloal over 3 years ago

graphql-api - RegulonDB-WS-API 1.2.2

The following changes were applied:

Fix

• Solved a bug related to an incorrectly named property

Update

• Updated mongodb-filter-object-parser library

- JavaScript
Published by andresloal over 3 years ago

graphql-api - RegulonDB-WS-API 1.2.1

This release contains the following changes:

Update

• Added Gensor Unit services in list as available service.

Fix

• Solved some properties with a wrong name in dbInfo Services
• Minor bugs fixed

- JavaScript
Published by andresloal over 3 years ago

graphql-api - RegulonDB-WS-API 1.2.0

This release contains the following changes:

New

• Added a first version of databaseInfo services, this services allows to user to known the metadata of the Regulon Datamarts data and all sources used to contain it.

Update

• Some models as Gene and Regulon were updated to allow new properties used in new requiriments of RegulonDB Web App
• Libraries updated

Fix

• Some bugs related to wrong data of responses were fixed
• Minor bugs fixed

- JavaScript
Published by andresloal over 3 years ago

graphql-api - RegulonDB-WS-API 1.1.2

The following changes were applied on GraphQL-API

Fix

• Solved a bug related to incorrect type of property in Gene Service

Update

• Added a new service to obtain all phrases associated to all Id's in object

- JavaScript
Published by andresloal over 3 years ago

graphql-api - RegulonDB-WS-API 1.1.1

Update

• Added continuants property on Regulon Service in regulatoryInteraction.regulator
• Bug fixes

- JavaScript
Published by andresloal almost 4 years ago

graphql-api - RegulonDB-WS-API 1.1.0

Update

• OpenServices and ClosedServices folders were renamed to Data and Tools respectively for better understanding of folder structure
• Schema and model of coexpression were updated, services are now correctly functional for deploy
• Moved Gensor Unit services from tools to data

Fix

• Minor bugs were solved

- JavaScript
Published by andresloal almost 4 years ago

graphql-api - RegulonDB-WS-API 1.0.2

Update

• Added products objects of Transcription Factor on Regulon Datamart

- JavaScript
Published by andresloal almost 4 years ago

graphql-api - RegulonDB-WS-API 1.0.1

Fix

• A bug related to asynchronous functions for mongoose was solved, now Queries are correctly functional again

- JavaScript
Published by andresloal about 4 years ago

graphql-api - RegulonDB-WS-API 1.0.0

Updated

• RegulonDB-WS-API now uses Apollo Server Express
• Libraries are up to date
• Added description for functions on controller's files

- JavaScript
Published by andresloal about 4 years ago

graphql-api - RegulonDB-WS-API 0.8.2

Fixed

• Merging schemas and resolvers code were changed due a recent update with GraphQL library (merge-graphql-schemas library is not more used, now @graphql-toolkit module is used)

- JavaScript
Published by andresloal over 4 years ago

graphql-api - RegulonDB-WS-API 0.8.1

Fix

• Improved function to test additional services in gateway, now if an additional service is unavailable, services will start without them

Update

• Updated libraries for RegulonDB Web Services

- JavaScript
Published by andresloal over 4 years ago

graphql-api - RegulonDB-WS-API 0.8.0

Update

• HT Services were removed from RegulonDB-WS-API repository, RegulonDB HT Services are available in the following repository https://github.com/regulondbunam/RegulonDBHT-API

- JavaScript
Published by andresloal over 4 years ago

graphql-api - RegulonDB-WS-API 0.7.1

Added

• New services were added to service list for use (Peaks, TFBinding and AuthorsData)

Updated

• Models of Peaks, TFBinding and AuthorsData were updated
• The model and schema were updated for Dataset Service

- JavaScript
Published by andresloal over 4 years ago

graphql-api - RegulonDB-WS-API 0.7.0

Added

• Web service for HT dataset was added to RegulonDB Web Services API, this service is now available for use in this release

Fixed

• Added tabs for playground page in open, closed and HT services
• Fixed bugs related to regulatory network services not allowing full responses due to name mismatch

- JavaScript
Published by andresloal over 4 years ago

graphql-api - RegulonDB-WS-API 0.6.0

Added

• Web service for Regulatory Network was added to RegulonDB Web Services API, this service is now available for use in this release

Fixed

• Improvement on dnaFeatures service controller, dealing with the queries in a better way
• Added compatibility with translationaltfbinding_sites for dnaFeatures services
• Minor bugs were solved in this version

- JavaScript
Published by andresloal over 4 years ago

graphql-api - RegulonDB-WS-API 0.5.2

Fixed

• Regulon model was updated on regulates -> genes -> terms, due an error that returns null even though the property exists in docs
• Improved error handling on Gateway server, with a specific format of errors (Message, Status, StatusCode)
• Updated name of id in Gene Datamart to _id to evade null responses

- JavaScript
Published by andresloal over 4 years ago

graphql-api - RegulonDB-WS-API 0.5.1

This version contains updates and resolves many situations that were not included in previous versions.

Updated

• The method to start services were updated to use only 1 instructions instead 2. Now is only necessary use "npm start"
• .env file were updated to include some details to use RegulonDB-GraphQL-API with Docker
• Added a genes object on properties of multifun and geneOntology on Regulon Service. This change can be viewed in this diagram: https://lucid.app/lucidchart/1be8ea06-41c6-4326-b249-aea80f10f2c2/view?page=~1FwrmR_wdzZ#

Fixed

• DnaFeatures query "getGeneticElementsFromInterval" was updated to include genetic objects that doesn't have positions and are linked to another genetic object, also were included instructions to obtain objects with no strand.
• Added _id property to transcriptionFactor object property on Regulon Service.

- JavaScript
Published by andresloal over 4 years ago

graphql-api - RegulonDB-WS-API 0.5.0

Added

• SRNA Service was added in its first version of datamart as a Data Open Service in RegulonDB GraphQL Web Services.
  • Some of this missing fields was:
  • Sigmulon - allCitations
  • Regulon - statistics
  • Operon - transcriptionUnits.promoters.boxes

Fixed

• Some bugs related to Regulon and Sigmulon services that cause missing fields on response were solved.

- JavaScript
Published by andresloal over 4 years ago

graphql-api - RegulonDB-WS-API 0.4.2

Release Notes

Fixed

• A bug related to citations of Regulatory Interactions in Operon Sevices was solver
• Some schemas were updated due a problem with the query example
• Some problems with HT services was solved (HT is not available in services list)

Updated

• A new version of Phrases Service was applied, this version is also available right now

- JavaScript
Published by andresloal almost 5 years ago

graphql-api - RegulonDB-WS-API 0.4.1

Release Notes

Fixed

• A bug related to Operon Service in Transcription Units -> Terminators were this fields resolve a null response has been solved

- JavaScript
Published by andresloal almost 5 years ago

graphql-api - RegulonDB-WS-API 0.4.0

Release Notes

Updated

• On all currently functional services were added a detailed description to Queries and assigned examples of use and a tag if a parameter is required for Web Service Documentation process.
• Added Citations on regulonDatamarts as allCitations and citations of transcriptionFactor

Added

• Sigmulon Service was added with its recently version of datamart as a Data Open Service in RegulonDB GraphQL Web Services.
• Added a first version of HT Service as a Data Open Service (this can be changed later)

- JavaScript
Published by andresloal almost 5 years ago

graphql-api - RegulonDB-WS-API 0.3.0

Release Notes

Updated

• On all currently functional services were added a detailed description to Queries and assigned default values on arguments that required for Web Service Documentation future process.

Added

• Regulon Service was added with its recently version of datamart as a Data Open Service in RegulonDB GraphQL Web Services.

- JavaScript
Published by andresloal almost 5 years ago

graphql-api - RegulonDB-WS-API 0.2.1

Release Notes

This release add changes applied on Operon Datamart such as:

• transcriptionFactorBindingSites property was renamed to regulatorBindingSites
• regulatorBindingSites on transcriptionUnits.genes was updated to support regulatoryInteractiones regulated by sRNA's
• mechanism property now appears on regulatorBindingSites Object

This changes was applied on datamarts diagrams

- JavaScript
Published by andresloal almost 5 years ago

graphql-api - RegulonDB-WS-API 0.2.0

This version contains latest version of gene and operon datamarts.

Some of the major changes are:

Gene

• Added fragments property on gene type for genes with multiple positions

Operon

• Operon is now in its latest version with changes applied on regulatorySites
• On TranscriptionUnit.genes were added the property transcriptionFactorBindingSites

- JavaScript
Published by andresloal about 5 years ago

graphql-api - RegulonDB-WS-API 0.1.1

This version solves mongodb connection problems.

- JavaScript
Published by andresloal about 5 years ago

graphql-api - RegulonDB-WS-API-Federation

This version contains a correct integration of Web Services developed by students in Internship Projects and a new folder structure to support Apollo-Federation services, separating Web Services in Open and Closed Services.

Functional services currently: Open services - Gene - Coexpression - Phrases

Closed services - DrawingTracesTool

Services in Development: - Operon (operon datamart v0.3 added but not final) - Regulon (not available)

- JavaScript
Published by andresloal about 5 years ago