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proper channel support for ncbimeta_annot
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| Original file line number | Diff line number | Diff line change |
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| # User Configuration Variables | ||
| OUTPUT_DIR : test | ||
| EMAIL : myusername@domain.com | ||
| API_KEY : | ||
| FORCE_PAUSE_SECONDS : 1 | ||
| DATABASE : test.sqlite | ||
|
|
||
| # NCBI Tables to Query | ||
| TABLES : | ||
| - Assembly | ||
| - BioSample | ||
| - BioProject | ||
| - SRA | ||
| - Nucleotide | ||
| - Pubmed | ||
|
|
||
| # Query Terms to Use | ||
| SEARCH_TERMS : | ||
| - Assembly : (SAMN12991206[BioSample]) | ||
| - BioProject : (PRJNA269675[BioProject IDs and Accessions]) | ||
| - BioSample: (SAMN12991206[Accession]) | ||
| - SRA : (SAMN12991206[BioSample]) | ||
| - Nucleotide : (SAMN12991206[BioSample]) | ||
| - Pubmed : (26634751[uid]) | ||
|
|
||
| # Columns of the database (ie. metadata fields to retrieve) | ||
| TABLE_COLUMNS : | ||
|
|
||
| - Assembly : | ||
| - AssemblyAccession : AssemblyAccession | ||
| - AssemblyBioSampleAccession : BioSampleAccn | ||
| - AssemblyBioSampleID : BioSampleId | ||
| - AssemblyGenbankBioprojectAccession : GB_BioProjects, BioprojectAccn | ||
| - AssemblyGenbankID : GbUid | ||
| - AssemblyRefseqBioprojectAccession : RS_BioProjects, BioprojectAccn | ||
| - AssemblyRefSeqCategory : RefSeq_category | ||
| - AssemblyRefSeqID : RsUid | ||
| - AssemblyWGSAccession : WGS | ||
| - AssemblyInfraspecies : InfraspeciesList, Sub_value | ||
| - AssemblyIsolate : Isolate | ||
| - AssemblyOrganism : Organism | ||
| - AssemblySpeciesTaxonomicID : SpeciesTaxid | ||
| - AssemblySpeciesName : SpeciesName | ||
| - AssemblyTaxonomicID : Taxid | ||
| - AssemblyName : AssemblyName | ||
| - AssemblyStatus : AssemblyStatus | ||
| - AssemblyType : AssemblyType | ||
| - AssemblyCoverage : Coverage | ||
| - AssemblyChromosomes : Meta, Stat, category, chromosome_count | ||
| - AssemblyContigCount: Meta, Stat, category, contig_count | ||
| - AssemblyContigN50 : Meta, Stat, category, contig_n50 | ||
| - AssemblyContigL50 : Meta, Stat, category, contig_l50 | ||
| - AssemblyNonChromosomalReplicons : Meta, Stat, category, non_chromosome_replicon_count | ||
| - AssemblyReplicons : Meta, Stat, category, replicon_count | ||
| - AssemblyScaffolds : Meta, Stat, category, scaffold_count | ||
| - AssemblyScaffoldN50 : Meta, Stat, category, scaffold_n50 | ||
| - AssemblyScaffoldL50 : Meta, Stat, category, scaffold_l50 | ||
| - AssemblyTotalLength : Meta, Stat, category, total_length | ||
| - AssemblyUngappedLength : Meta, Stat, category, ungapped_length | ||
| - AssemblySubmitterOrganization : SubmitterOrganization | ||
| - AssemblySubmissionDate : SubmissionDate | ||
| - AssemblyReleaseDate : SeqReleaseDate | ||
| - AssemblyFTPAssemblyReport : FtpPath_Assembly_rpt | ||
| - AssemblyFTPGenbank : FtpPath_GenBank | ||
| - AssemblyFTPRefSeq : FtpPath_RefSeq | ||
| - AssemblyFTPStatsReport : FtpPath_Stats_rpt | ||
| - AssemblyComment : NullValue | ||
|
|
||
| - BioSample : | ||
| - BioSampleAccession: BioSample, accession | ||
| - BioSampleAccessionSecondary: NullValue | ||
| - BioSampleBioProjectAccession: XPATH, //Links/Link[@target='bioproject']/@label | ||
| - BioSampleSRAAccession: Id, db, SRA | ||
| - BioSampleTitle: Title | ||
| - BioSampleName: Id, db_label, Sample name | ||
| - BioSampleType: Attribute, harmonized_name, sample_type | ||
| - BioSamplePackage: Package | ||
| - BioSampleInfraspecies: Infraspecies | ||
| - BioSampleOrganism: Description, OrganismName | ||
| - BioSampleOrganismAlt: Description, Organism, taxonomy_name | ||
| - BioSampleSubSpecies: Attribute, harmonized_name, sub_species | ||
| - BioSampleStrain: Attribute, harmonized_name, strain | ||
| - BioSampleTaxonomyID: Organism, taxonomy_id | ||
| - BioSampleBiovar: Attribute, harmonized_name, biovar | ||
| - BioSampleSerovar: Attribute, harmonized_name, serovar | ||
| - BioSampleCollectionDate: Attribute, harmonized_name, collection_date | ||
| - BioSampleGeographicLocation: Attribute, harmonized_name, geo_loc_name | ||
| - BioSampleHost: Attribute, harmonized_name, host | ||
| - BioSampleHostDisease : Attribute, harmonized_name, host_disease | ||
| - BioSampleHostHealthState : Attribute, harmonized_name, host_health_state | ||
| - BioSampleIsolateNameAlias: Attribute, harmonized_name, isolate_name_alias | ||
| - BioSampleIsolationSource: Attribute, harmonized_name, isolation_source | ||
| - BioSampleLat : Attribute, attribute_name, Latitude | ||
| - BioSampleLatLon : Attribute, harmonized_name, lat_lon | ||
| - BioSampleLon : Attribute, attribute_name, Longitude | ||
| - BioSampleSubmissionDate: BioSample, submission_date | ||
| - BioSampleModificationDate: BioSample, last_update | ||
| - BioSamplePublicationDate: BioSample, publication_date | ||
| - BioSampleOrganization: Owner, Name | ||
| - BioSampleComment : NullValue | ||
|
|
||
| - BioProject : | ||
| - BioProjectAccession : ArchiveID, accession | ||
| - BioProjectDataType : ProjectDataTypeSet, DataType | ||
| - BioProjectDescription : ProjectDescr, Description | ||
| - BioProjectMethodType : Method, method_type | ||
| - BioProjectName : ProjectDescr, Name | ||
| - BioProjectTargetCapture : Target, capture | ||
| - BioProjectTargetMaterial : Target, material | ||
| - BioProjectTargetScope : Target, sample_scope | ||
| - BioProjectTitle : XPATH, //ProjectDescr/Title/text() | ||
| - BioProjectOrganismLabel : ProjectTypeSubmission, Label | ||
| - BioProjectOrganismStrain : ProjectTypeSubmission, Strain | ||
| - BioProjectOrganismTaxID : ProjectTypeSubmission, Organism, taxID | ||
| - BioProjectSpeciesTaxID : ProjectTypeSubmission, Organism, species | ||
| - BioProjectSupergroup : ProjectTypeSubmission, Supergroup | ||
| - BioProjectRegistrationDate : Submission, submitted | ||
| - BioProjectReleaseDate: ProjectReleaseDate | ||
| - BioProjectModificationDate: Submission, last_update | ||
| - BioProjectRelevanceMedical : Relevance, Medical | ||
| - BioProjectSubmitterOrganization : Organization, Name | ||
| - BioProjectPublished: Publication, status | ||
| - BioProjectDatePublished: Publication, date | ||
| - BioProjectPublicationID: Publication, id | ||
| - BioProjectPublicationDB: Publication, DbType | ||
| - BioProjectComment : NullValue | ||
|
|
||
| - Nucleotide : | ||
| - NucleotideAccession : GBSeq_primary-accession | ||
| - NucleotideAccessionVersion : GBSeq_accession-version | ||
| - NucleotideBioSampleAccession: XPATH, //GBXref[GBXref_dbname/text() = 'BioSample']/GBXref_id | ||
| - NucleotideBioProjectAccession : GBSeq_project | ||
| - NucleotideOrganism : GBSeq_organism | ||
| - NucleotideTaxonomy : GBSeq_taxonomy | ||
| - NucleotideDefinition : GBSeq_definition | ||
| - NucleotideDivision : GBSeq_division | ||
| - NucleotideReferenceJournal: GBSeq_references, GBReference_journal | ||
| - NucleotideReferenceTitle : GBSeq_references, GBReference_title | ||
| - NucleotideReferenceAuthors : GBSeq_references, GBReference_authors, GBAuthor | ||
| - NucleotideLength : GBSeq_length | ||
| - NucleotideMoleculeType : GBSeq_moltype | ||
| - NucleotideSeqDataName : GBSeq_alt-seq, GBAltSeqData_name | ||
| - NucleotideSource : GBSeq_source | ||
| - NucleotideStrandedness : GBSeq_strandedness | ||
| - NucleotideTopology : GBSeq_topology | ||
| - NucleotideCreateDate : GBSeq_create-date | ||
| - NucleotideUpdateDate : GBSeq_update-date | ||
| - NucleotideGenBankComment : GBSeq_comment | ||
| - NucleotideAnnotationDate: Annotation Date | ||
| - NucleotideAnnotationMethod: Annotation Method | ||
| - NucleotideAnnotationPipeline: Annotation Pipeline | ||
| - NucleotideAnnotationProvider: Annotation Provider | ||
| - NucleotideAnnotationSoftwarerevision: Annotation Software revision | ||
| - NucleotideAssemblyDate: Assembly Date | ||
| - NucleotideAssemblyMethod: Assembly Method | ||
| - NucleotideAssemblyName: Assembly Name | ||
| - NucleotideCDS: CDS | ||
| - NucleotideCDSTotal: CDS (total) | ||
| - NucleotideCDSCoding: CDS (coding) | ||
| - NucleotideCDSProtein: CDS (with protein) | ||
| - NucleotideCDSWithoutProtein: CDS (without protein) | ||
| - NucleotideCRISPRArrays: CRISPR Arrays | ||
| - NucleotideExpectedFinalVersion: Expected Final Version | ||
| - NucleotideFeaturesAnnotated: Features Annotated | ||
| - NucleotideGenes: Genes | ||
| - NucleotideGenesTotal: Genes (total) | ||
| - NucleotideGenesCoding: Genes (coding) | ||
| - NucleotideGenesRNA: Genes (RNA) | ||
| - NucleotideGenomeCoverage: Genome Coverage | ||
| - NucleotideGenomeRepresentation: Genome Representation | ||
| - NucleotidencRNAs: ncRNAs | ||
| - NucleotidePseudoGenes: Pseudo Genes | ||
| - NucleotidePseudoGenesTotal: Pseudo Genes (total) | ||
| - NucleotidePseudoGenesAmbResidues: Pseudo Genes (ambiguous residues) | ||
| - NucleotidePseudoGenesFrameshifted: Pseudo Genes (frameshifted) | ||
| - NucleotidePseudoGenesIncomplete: Pseudo Genes (incomplete) | ||
| - NucleotidePseudoGenesInternalStop: Pseudo Genes (internal stop) | ||
| - NucleotidePseudoGenesMultipleProblems: Pseudo Genes (multiple problems) | ||
| - NucleotiderRNAs: rRNAs | ||
| - NucleotiderRNAsComplete: complete rRNAs | ||
| - NucleotiderRNAsPartial: partial rRNAs | ||
| - NucleotideSequencingTechnology: Sequencing Technology | ||
| - NucleotideRNAs: tRNAs | ||
| - NucleotideComment : NullValue | ||
|
|
||
| - SRA : | ||
| - SRABioProjectAccession : STUDY, EXTERNAL_ID, namespace, BioProject | ||
| - SRABioSampleAccession : RUN_SET, RUN, Pool, EXTERNAL_ID, namespace, BioSample | ||
| - SRASampleAccession : SAMPLE_DESCRIPTOR, accession | ||
| - SRASampleName : SAMPLE, alias | ||
| - SRAExperimentAccession : EXPERIMENT, accession | ||
| - SRAExperimentName : EXPERIMENT, alias | ||
| - SRARunAccession : RUN, accession | ||
| - SRARunName : RUN, alias | ||
| - SRAIsPublic : RUN, is_public | ||
| - SRAStaticDataAvailable : RUN, static_data_available | ||
| - SRAStudyAcc : STUDY, accession | ||
| - SRAStudyName : STUDY_TITLE | ||
| - SRAStudyAbstract: STUDY_ABSTRACT | ||
| - SRAOrganismName : SAMPLE_NAME, SCIENTIFIC_NAME | ||
| - SRAOrganismTaxID : SAMPLE, TAXON_ID | ||
| - SRAClusterName : RUN, cluster_name | ||
| - SRAPlatform : PLATFORM | ||
| - SRAInstrumentModel : PLATFORM, INSTRUMENT_MODEL | ||
| - SRALibraryName : LIBRARY_NAME | ||
| - SRALibraryLayout : LIBRARY_LAYOUT | ||
| - SRALibrarySelection : LIBRARY_SELECTION | ||
| - SRALibrarySource : LIBRARY_SOURCE | ||
| - SRALibraryStrategy : LIBRARY_STRATEGY | ||
| - SRATotalBases : RUN_SET, RUN, total_bases | ||
| - SRATotalSize : RUN_SET, RUN, size | ||
| - SRATotalSpots : RUN_SET, RUN, total_spots | ||
| - SRAFileUrl : SRAFile, url | ||
| - SRAFileName : SRAFile, filename | ||
| - SRAFileSize : SRAFile, size | ||
| - SRAFileType : SRAFile, semantic_name | ||
| - SRARunPublishDate : RUN_SET, RUN, published | ||
| - SRACenterName : SUBMISSION, center_name | ||
| - SRAContactEmail : Organization, Contact, email | ||
| - SRALabName : SUBMISSION, lab_name | ||
| - SRASubmitterAccession : SUBMISSION, accession | ||
| - SRAComment : NullValue | ||
|
|
||
| - Pubmed : | ||
| - PubmedPublishYear : PubDate, Year | ||
| - PubmedPubishMonth : PubDate, Month | ||
| - PubmedPublishDay : PubDate, Day | ||
| - PubmedEPublishDate : EPubDate | ||
| - PubmedPublishModel : Article, PubModel | ||
| - PubmedType : PublicationType | ||
| - PubmedJournalTitle : Journal, Title | ||
| - PubmedJournalAbbrev : Journal, ISOAbbreviation | ||
| - PubmedJournalISSN : Journal, ISSN | ||
| - PubmedArticleTitle : ArticleTitle | ||
| - PubmedAbstract : AbstractText | ||
| - PubmedVolume : Volume | ||
| - PubmedIssue : Issue | ||
| - PubmedPages : MedlinePgn | ||
| - PubmedDOI : ELocationID, EIdType, doi | ||
| - PubmedAuthorsLastName : AuthorList, LastName | ||
| - PubmedAuthorsForeName : AuthorList, ForeName | ||
| - PubmedAuthorsAffiliation : AuthorList, Affiliation | ||
| - PubmedLanguage : Language | ||
| - PubmedCitations : Reference, Citation | ||
| - PubmedRecordStatus : MedlineCitation, Status | ||
| - PubmedPubStatus : PublicationStatus | ||
| - PubmedComment : NullValue |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| BioSampleAccession BioSampleHostDisease BioSampleCollectionDate | ||
| SAMN12991206 Plague 1984 | ||
| MissingAccession123 MissingDisease MissingDate |
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