Ecosyste.ms: Issues

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GitHub / opencb/bionetdb issues and pull requests

#73 - build(deps): bump jackson-databind from 2.10.1 to 2.12.7.1

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#73 - build(deps): bump jackson-databind from 2.10.1 to 2.12.7.1

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#72 - build(deps): bump jackson-databind from 2.10.1 to 2.13.4.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#72 - build(deps): bump jackson-databind from 2.10.1 to 2.13.4.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#71 - build(deps): bump jackson-databind from 2.10.1 to 2.12.6.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#70 - Compress CSV files

Issue - State: open - Opened by jtarraga almost 4 years ago
Labels: enhancement

#70 - Compress CSV files

Issue - State: open - Opened by jtarraga almost 4 years ago
Labels: enhancement

#70 - Compress CSV files

Issue - State: open - Opened by jtarraga almost 4 years ago
Labels: enhancement

#69 - build(deps): bump jackson.version from 2.10.1 to 2.12.1

Pull Request - State: open - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#69 - build(deps): bump jackson.version from 2.10.1 to 2.12.1

Pull Request - State: open - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#69 - build(deps): bump jackson.version from 2.10.1 to 2.12.1

Pull Request - State: open - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#68 - Improve node and relation objects

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#67 - Rename relations and nodes related to SAMPLE node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#67 - Rename relations and nodes related to SAMPLE node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#66 - Rename relations and nodes related to VARIANT node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#66 - Rename relations and nodes related to VARIANT node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#65 - Rename relations and nodes related to TRANSCRIPT node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#65 - Rename relations and nodes related to TRANSCRIPT node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#65 - Rename relations and nodes related to TRANSCRIPT node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#64 - Rename relations and nodes related to PROTEIN node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#64 - Rename relations and nodes related to PROTEIN node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#63 - Rename relations and nodes related to GENE node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#62 - Modify BioNetDB data model: Node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#62 - Modify BioNetDB data model: Node

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#61 - Add/update methods to load/modify nodes/relations in an existing BioNetDB database

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement, feature

#61 - Add/update methods to load/modify nodes/relations in an existing BioNetDB database

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement, feature

#61 - Add/update methods to load/modify nodes/relations in an existing BioNetDB database

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement, feature

#60 - Update the property "source" in the BioNetDB data models: Node and Relation

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#60 - Update the property "source" in the BioNetDB data models: Node and Relation

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: enhancement

#59 - Implement BioNetDB executors and web services focussed on nodes, paths and networks

Issue - State: closed - Opened by jtarraga about 4 years ago
Labels: feature, task

#58 - Add CLI parameters: --add-network-file, --add-variant-file...

Issue - State: open - Opened by jtarraga about 4 years ago
Labels: enhancement, feature, task

#58 - Add CLI parameters: --add-network-file, --add-variant-file...

Issue - State: open - Opened by jtarraga about 4 years ago
Labels: enhancement, feature, task

#57 - Add support for RefSeq genes and transcripts

Issue - State: closed - Opened by jtarraga over 4 years ago
Labels: enhancement, task

#57 - Add support for RefSeq genes and transcripts

Issue - State: closed - Opened by jtarraga over 4 years ago
Labels: enhancement, task

#57 - Add support for RefSeq genes and transcripts

Issue - State: closed - Opened by jtarraga over 4 years ago
Labels: enhancement, task

#56 - Update BioNetDB nodes/relations according to the Biodata data model changes

Issue - State: closed - Opened by jtarraga over 4 years ago
Labels: enhancement

#56 - Update BioNetDB nodes/relations according to the Biodata data model changes

Issue - State: closed - Opened by jtarraga over 4 years ago
Labels: enhancement

#55 - Command line for admin tasks: bionetdb-admin.sh

Issue - State: closed - Opened by jtarraga over 4 years ago
Labels: enhancement, task

#54 - build(deps): bump junit from 4.12 to 4.13.1

Pull Request - State: open - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#54 - build(deps): bump junit from 4.12 to 4.13.1

Pull Request - State: open - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#53 - Load clinical analysis into BioNetDB (Neo4J database)

Issue - State: open - Opened by jtarraga over 5 years ago
Labels: enhancement, feature, task

#53 - Load clinical analysis into BioNetDB (Neo4J database)

Issue - State: open - Opened by jtarraga over 5 years ago
Labels: enhancement, feature, task

#52 - core: genotype handling in ProtSystAnalysis set one level up

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#52 - core: genotype handling in ProtSystAnalysis set one level up

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#51 - implement VariantIterator interface

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#51 - implement VariantIterator interface

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#49 - proteinSystem implementation

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#49 - proteinSystem implementation

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#48 - core: deNovo and CompoundHeterozygous support

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#48 - core: deNovo and CompoundHeterozygous support

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#48 - core: deNovo and CompoundHeterozygous support

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#47 - BioNetDB variant filter API creation

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#47 - BioNetDB variant filter API creation

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#46 - Support for variant retrieval according to their mode of inheritance:…

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#46 - Support for variant retrieval according to their mode of inheritance:…

Pull Request - State: closed - Opened by roldanx almost 6 years ago

#45 - fit xQuery output with VRConverter input

Pull Request - State: closed - Opened by roldanx about 6 years ago - 1 comment

#45 - fit xQuery output with VRConverter input

Pull Request - State: closed - Opened by roldanx about 6 years ago - 1 comment

#44 - Major xQuery changes

Pull Request - State: closed - Opened by roldanx about 6 years ago

#44 - Major xQuery changes

Pull Request - State: closed - Opened by roldanx about 6 years ago

#44 - Major xQuery changes

Pull Request - State: closed - Opened by roldanx about 6 years ago

#43 - neo4j tiering developed

Pull Request - State: closed - Opened by roldanx over 6 years ago

#43 - neo4j tiering developed

Pull Request - State: closed - Opened by roldanx over 6 years ago

#42 - Basic variant analysis created (Dominant. recessive, de novo, compund heterozygote...)

Pull Request - State: closed - Opened by roldanx over 6 years ago
Labels: enhancement

#42 - Basic variant analysis created (Dominant. recessive, de novo, compund heterozygote...)

Pull Request - State: closed - Opened by roldanx over 6 years ago
Labels: enhancement

#41 - Fix bug so that node webservices return node properties

Issue - State: closed - Opened by jtarraga over 6 years ago
Labels: bug

#41 - Fix bug so that node webservices return node properties

Issue - State: closed - Opened by jtarraga over 6 years ago
Labels: bug

#40 - Fix duplicated genes in CSV file when importing data

Issue - State: closed - Opened by jtarraga over 6 years ago
Labels: bug

#40 - Fix duplicated genes in CSV file when importing data

Issue - State: closed - Opened by jtarraga over 6 years ago
Labels: bug

#39 - Remove duplicated GENE - DRUG relationships

Issue - State: closed - Opened by jtarraga over 6 years ago
Labels: bug

#39 - Remove duplicated GENE - DRUG relationships

Issue - State: closed - Opened by jtarraga over 6 years ago
Labels: bug

#38 - Add microRNA information to the BioNetDB data model

Issue - State: closed - Opened by jtarraga over 6 years ago
Labels: enhancement, feature

#38 - Add microRNA information to the BioNetDB data model

Issue - State: closed - Opened by jtarraga over 6 years ago
Labels: enhancement, feature

#37 - Data models documentation

Issue - State: closed - Opened by jtarraga over 6 years ago - 1 comment
Labels: enhancement

#36 - Implement command line to import data into BioNetDB

Issue - State: closed - Opened by jtarraga over 6 years ago
Labels: enhancement, task

#36 - Implement command line to import data into BioNetDB

Issue - State: closed - Opened by jtarraga over 6 years ago
Labels: enhancement, task

#35 - Filter BioPAX xrefs before inserting into the network database

Issue - State: closed - Opened by jtarraga almost 7 years ago
Labels: enhancement

#35 - Filter BioPAX xrefs before inserting into the network database

Issue - State: closed - Opened by jtarraga almost 7 years ago
Labels: enhancement

#34 - Create Pathway nodes when loading BioPAX files

Issue - State: closed - Opened by jtarraga almost 7 years ago
Labels: feature, task

#34 - Create Pathway nodes when loading BioPAX files

Issue - State: closed - Opened by jtarraga almost 7 years ago
Labels: feature, task

#33 - BioPax loading by transaction batches

Issue - State: closed - Opened by jtarraga almost 7 years ago
Labels: enhancement, task

#33 - BioPax loading by transaction batches

Issue - State: closed - Opened by jtarraga almost 7 years ago
Labels: enhancement, task

#32 - Create a 'configuration' node

Issue - State: closed - Opened by jtarraga almost 7 years ago
Labels: task

#32 - Create a 'configuration' node

Issue - State: closed - Opened by jtarraga almost 7 years ago
Labels: task

#31 - Remove defaultDatabase from configuration file

Issue - State: closed - Opened by imedina almost 7 years ago
Labels: task

#30 - Rename Path to NetworkPath

Issue - State: closed - Opened by imedina almost 7 years ago
Labels: enhancement

#30 - Rename Path to NetworkPath

Issue - State: closed - Opened by imedina almost 7 years ago
Labels: enhancement

#29 - Implement a REST API to query networks

Issue - State: closed - Opened by imedina almost 7 years ago
Labels: REST

#28 - Bug in NetworkDBAdaptor Implementation

Issue - State: closed - Opened by Swaathik over 8 years ago

#28 - Bug in NetworkDBAdaptor Implementation

Issue - State: closed - Opened by Swaathik over 8 years ago

#27 - Add Maven CheckStyle plugin

Issue - State: closed - Opened by imedina over 9 years ago
Labels: enhancement, task

#27 - Add Maven CheckStyle plugin

Issue - State: closed - Opened by imedina over 9 years ago
Labels: enhancement, task

#26 - Generate a queryBuilder method

Issue - State: open - Opened by pfurio over 9 years ago
Labels: task

#25 - Override the equals method in the PhysicalEntity class

Issue - State: closed - Opened by pfurio over 9 years ago
Labels: enhancement

#25 - Override the equals method in the PhysicalEntity class

Issue - State: closed - Opened by pfurio over 9 years ago
Labels: enhancement

#24 - Create method to retrieve a summary of the database status

Issue - State: closed - Opened by pfurio over 9 years ago
Labels: enhancement

#24 - Create method to retrieve a summary of the database status

Issue - State: closed - Opened by pfurio over 9 years ago
Labels: enhancement

#23 - build.sh can be implemented using Maven ant plugin

Issue - State: closed - Opened by imedina over 9 years ago
Labels: task

#22 - Added proper tests for the methods of Neo4JNetworkDBAdaptor class

Pull Request - State: closed - Opened by pfurio over 9 years ago