HCA Data Portal

Analysis protocol

Information about the analysis protocol.

View JSON source: analysis_protocoldoneShow required fields only


Alignment softwareanalysis_protocol.alignment_softwarecopy (string) Name of alignment software used to map FASTQ files to reference genome. For example "Cellranger", "kallisto bustools", "GSNAP" or "STAR".
Alignment software versionanalysis_protocol.alignment_software_versioncopy (string) Version of alignment software used to map FASTQ files to reference genome. For example "v2.0.1", "2.4.2a" or "v0.45.2".
Computational methodanalysis_protocol.computational_methodcopy (string) A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository. For example "SmartSeq2SingleCell" or "10x".
Gene annotation versionanalysis_protocol.gene_annotation_versioncopy (string) The Ensembl release version accession number or NCBI RefSeq assembly version used for gene annotation. For example "v110", "GCF_000001405.40" or "GCF_000001635.27".
Intron inclusionanalysis_protocol.intron_inclusioncopy (boolean) Whether introns were included in the alignment process during read counting. For example "Should be one of: yes, or no.".
Analysis protocol>Matrix (matrix object) Information related to protocols that output a matrix.
Data normalization method(s)analysis_protocol.matrix.data_normalization_methodscopy (array from matrix) Method(s) used to normalize data in the matrix
Derivation processanalysis_protocol.matrix.derivation_processcopy (array from matrix) Type of computational tool used in generating the matrix object.
Analysis protocol>Protocol typeRequired (process_type_ontology object) The type of protocol.
Process type ontology IDanalysis_protocol.type.ontologycopy (string from process_type_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0009128" or "EFO:0009121".Graph restriction: Subclasses of EFO:0002694 from obo:efo.
Process type ontology labelanalysis_protocol.type.ontology_labelcopy (string from process_type_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "enzymatic dissociation" or "blood draw".
Process typeRequiredanalysis_protocol.type.textcopy (string from process_type_ontology) The name of a process type being used. For example "enzymatic dissociation" or "blood draw".
Analysis protocol>Protocol coreRequired (protocol_core object) Core protocol-level information.
Document filenameanalysis_protocol.protocol_core.documentcopy (string from protocol_core) A filename of a PDF document containing the details of the protocol. For example "my_cool_protocol.pdf".
Protocol descriptionanalysis_protocol.protocol_core.protocol_descriptioncopy (string from protocol_core) A general description of the protocol.
Protocol IDRequiredanalysis_protocol.protocol_core.protocol_idcopy (string from protocol_core) A unique ID for the protocol.
Protocol nameanalysis_protocol.protocol_core.protocol_namecopy (string from protocol_core) A short name for the protocol.
protocols.io DOIanalysis_protocol.protocol_core.protocols_io_doicopy (string from protocol_core) The protocols.io digital object identifier (doi) for the protocol. For example "10.17504/protocols.io.mgjc3un".
Publication DOIanalysis_protocol.protocol_core.publication_doicopy (string from protocol_core) The publication digital object identifier (doi) for the protocol. For example "10.1101/193219".
Analysis protocol>provenance (provenance object) Provenance information provided by the system.
Accessionanalysis_protocol.provenance.accessioncopy (string from provenance) A unique accession for this entity, provided by the broker.
Document IDRequiredanalysis_protocol.provenance.document_idcopy (string from provenance) Identifier for document.
Schema major versionanalysis_protocol.provenance.schema_major_versioncopy (integer from provenance) The major version number of the schema. For example "4" or "10".
Schema minor versionanalysis_protocol.provenance.schema_minor_versioncopy (integer from provenance) The minor version number of the schema. For example "6" or "15".
Submission dateRequiredanalysis_protocol.provenance.submission_datecopy (string from provenance) When project was first submitted to database.
Submitter IDanalysis_protocol.provenance.submitter_idcopy (string from provenance) ID of individual who first submitted project.
Update dateanalysis_protocol.provenance.update_datecopy (string from provenance) When project was last updated.
Updater IDanalysis_protocol.provenance.updater_idcopy (string from provenance) ID of individual who last updated project.