Constants

Constants are used internally to ensure consistent use of keywords when parsing and writing investigation, study and assay files (in particular in the headers). They can also be used when creating a model from scratch, i.e. to provide a desired header order (used for writing) when creating study/assay nodes or investigation sections (or section entries).

Investigation Headers

Constants of valid vertical row headers for investigation parsing and writing, as specified in the ISA-Tab investigation specifications.

altamisa.constants.investigation_headers.ONTOLOGY_SOURCE_REFERENCE = 'ONTOLOGY SOURCE REFERENCE'

altamisa.constants.investigation_headers.INVESTIGATION = 'INVESTIGATION'

altamisa.constants.investigation_headers.INVESTIGATION_PUBLICATIONS = 'INVESTIGATION PUBLICATIONS'

altamisa.constants.investigation_headers.INVESTIGATION_CONTACTS = 'INVESTIGATION CONTACTS'

altamisa.constants.investigation_headers.STUDY = 'STUDY'

altamisa.constants.investigation_headers.STUDY_DESIGN_DESCRIPTORS = 'STUDY DESIGN DESCRIPTORS'

altamisa.constants.investigation_headers.STUDY_PUBLICATIONS = 'STUDY PUBLICATIONS'

altamisa.constants.investigation_headers.STUDY_FACTORS = 'STUDY FACTORS'

altamisa.constants.investigation_headers.STUDY_ASSAYS = 'STUDY ASSAYS'

altamisa.constants.investigation_headers.STUDY_PROTOCOLS = 'STUDY PROTOCOLS'

altamisa.constants.investigation_headers.STUDY_CONTACTS = 'STUDY CONTACTS'

altamisa.constants.investigation_headers.TERM_SOURCE_NAME = 'Term Source Name'

altamisa.constants.investigation_headers.TERM_SOURCE_FILE = 'Term Source File'

altamisa.constants.investigation_headers.TERM_SOURCE_VERSION = 'Term Source Version'

altamisa.constants.investigation_headers.TERM_SOURCE_DESCRIPTION = 'Term Source Description'

altamisa.constants.investigation_headers.ONTOLOGY_SOURCE_REF_KEYS = ('Term Source Name', 'Term Source File', 'Term Source Version', 'Term Source Description')

Collected header keys of ONTOLOGY SOURCE REFERENCE section

altamisa.constants.investigation_headers.INVESTIGATION_IDENTIFIER = 'Investigation Identifier'

altamisa.constants.investigation_headers.INVESTIGATION_TITLE = 'Investigation Title'

altamisa.constants.investigation_headers.INVESTIGATION_DESCRIPTION = 'Investigation Description'

altamisa.constants.investigation_headers.INVESTIGATION_SUBMISSION_DATE = 'Investigation Submission Date'

altamisa.constants.investigation_headers.INVESTIGATION_PUBLIC_RELEASE_DATE = 'Investigation Public Release Date'

altamisa.constants.investigation_headers.INVESTIGATION_INFO_KEYS = ('Investigation Identifier', 'Investigation Title', 'Investigation Description', 'Investigation Submission Date', 'Investigation Public Release Date')

Collected header keys of INVESTIGATION section

altamisa.constants.investigation_headers.INVESTIGATION_PUBMED_ID = 'Investigation PubMed ID'

altamisa.constants.investigation_headers.INVESTIGATION_PUBLICATION_DOI = 'Investigation Publication DOI'

altamisa.constants.investigation_headers.INVESTIGATION_PUBLICATION_AUTHOR_LIST = 'Investigation Publication Author List'

altamisa.constants.investigation_headers.INVESTIGATION_PUBLICATION_TITLE = 'Investigation Publication Title'

altamisa.constants.investigation_headers.INVESTIGATION_PUBLICATION_STATUS = 'Investigation Publication Status'

altamisa.constants.investigation_headers.INVESTIGATION_PUBLICATIONS_KEYS = ('Investigation PubMed ID', 'Investigation Publication DOI', 'Investigation Publication Author List', 'Investigation Publication Title', 'Investigation Publication Status', 'Investigation Publication Status Term Accession Number', 'Investigation Publication Status Term Source REF')

Collected header keys of INVESTIGATION PUBLICATIONS

altamisa.constants.investigation_headers.INVESTIGATION_PERSON_LAST_NAME = 'Investigation Person Last Name'

altamisa.constants.investigation_headers.INVESTIGATION_PERSON_FIRST_NAME = 'Investigation Person First Name'

altamisa.constants.investigation_headers.INVESTIGATION_PERSON_MID_INITIALS = 'Investigation Person Mid Initials'

altamisa.constants.investigation_headers.INVESTIGATION_PERSON_EMAIL = 'Investigation Person Email'

altamisa.constants.investigation_headers.INVESTIGATION_PERSON_PHONE = 'Investigation Person Phone'

altamisa.constants.investigation_headers.INVESTIGATION_PERSON_FAX = 'Investigation Person Fax'

altamisa.constants.investigation_headers.INVESTIGATION_PERSON_ADDRESS = 'Investigation Person Address'

altamisa.constants.investigation_headers.INVESTIGATION_PERSON_AFFILIATION = 'Investigation Person Affiliation'

altamisa.constants.investigation_headers.INVESTIGATION_PERSON_ROLES = 'Investigation Person Roles'

altamisa.constants.investigation_headers.INVESTIGATION_PERSON_ROLES_TERM_SOURCE_REF = 'Investigation Person Roles Term Source REF'

altamisa.constants.investigation_headers.INVESTIGATION_CONTACTS_KEYS = ('Investigation Person Last Name', 'Investigation Person First Name', 'Investigation Person Mid Initials', 'Investigation Person Email', 'Investigation Person Phone', 'Investigation Person Fax', 'Investigation Person Address', 'Investigation Person Affiliation', 'Investigation Person Roles', 'Investigation Person Roles Term Accession Number', 'Investigation Person Roles Term Source REF')

Collected header keys of INVESTIGATION CONTACTS section

altamisa.constants.investigation_headers.STUDY_IDENTIFIER = 'Study Identifier'

altamisa.constants.investigation_headers.STUDY_TITLE = 'Study Title'

altamisa.constants.investigation_headers.STUDY_DESCRIPTION = 'Study Description'

altamisa.constants.investigation_headers.STUDY_SUBMISSION_DATE = 'Study Submission Date'

altamisa.constants.investigation_headers.STUDY_PUBLIC_RELEASE_DATE = 'Study Public Release Date'

altamisa.constants.investigation_headers.STUDY_FILE_NAME = 'Study File Name'

altamisa.constants.investigation_headers.STUDY_INFO_KEYS = ('Study Identifier', 'Study Title', 'Study Description', 'Study Submission Date', 'Study Public Release Date', 'Study File Name')

Collected header keys of STUDY section

altamisa.constants.investigation_headers.STUDY_DESIGN_TYPE = 'Study Design Type'

altamisa.constants.investigation_headers.STUDY_DESIGN_TYPE_TERM_ACCESSION_NUMBER = 'Study Design Type Term Accession Number'

altamisa.constants.investigation_headers.STUDY_DESIGN_TYPE_TERM_SOURCE_REF = 'Study Design Type Term Source REF'

altamisa.constants.investigation_headers.STUDY_DESIGN_DESCR_KEYS = ('Study Design Type', 'Study Design Type Term Accession Number', 'Study Design Type Term Source REF')

Collected header keys of STUDY DESIGN DESCRIPTORS section

altamisa.constants.investigation_headers.STUDY_PUBMED_ID = 'Study PubMed ID'

altamisa.constants.investigation_headers.STUDY_PUBLICATION_DOI = 'Study Publication DOI'

altamisa.constants.investigation_headers.STUDY_PUBLICATION_AUTHOR_LIST = 'Study Publication Author List'

altamisa.constants.investigation_headers.STUDY_PUBLICATION_TITLE = 'Study Publication Title'

altamisa.constants.investigation_headers.STUDY_PUBLICATION_STATUS = 'Study Publication Status'

altamisa.constants.investigation_headers.STUDY_PUBLICATION_STATUS_TERM_SOURCE_REF = 'Study Publication Status Term Source REF'

altamisa.constants.investigation_headers.STUDY_PUBLICATIONS_KEYS = ('Study PubMed ID', 'Study Publication DOI', 'Study Publication Author List', 'Study Publication Title', 'Study Publication Status', 'Study Publication Status Term Accession Number', 'Study Publication Status Term Source REF')

Collected header keys of STUDY PUBLICATIONS section

altamisa.constants.investigation_headers.STUDY_FACTOR_NAME = 'Study Factor Name'

altamisa.constants.investigation_headers.STUDY_FACTOR_TYPE = 'Study Factor Type'

altamisa.constants.investigation_headers.STUDY_FACTOR_TYPE_TERM_ACCESSION_NUMBER = 'Study Factor Type Term Accession Number'

altamisa.constants.investigation_headers.STUDY_FACTOR_TYPE_TERM_SOURCE_REF = 'Study Factor Type Term Source REF'

altamisa.constants.investigation_headers.STUDY_FACTORS_KEYS = ('Study Factor Name', 'Study Factor Type', 'Study Factor Type Term Accession Number', 'Study Factor Type Term Source REF')

Collected header keys of STUDY FACTORS section

altamisa.constants.investigation_headers.STUDY_ASSAY_FILE_NAME = 'Study Assay File Name'

altamisa.constants.investigation_headers.STUDY_ASSAY_MEASUREMENT_TYPE = 'Study Assay Measurement Type'

altamisa.constants.investigation_headers.STUDY_ASSAY_MEASUREMENT_TYPE_TERM_SOURCE_REF = 'Study Assay Measurement Type Term Source REF'

altamisa.constants.investigation_headers.STUDY_ASSAY_TECHNOLOGY_TYPE = 'Study Assay Technology Type'

altamisa.constants.investigation_headers.STUDY_ASSAY_TECHNOLOGY_TYPE_TERM_SOURCE_REF = 'Study Assay Technology Type Term Source REF'

altamisa.constants.investigation_headers.STUDY_ASSAY_TECHNOLOGY_PLATFORM = 'Study Assay Technology Platform'

altamisa.constants.investigation_headers.STUDY_ASSAYS_KEYS = ('Study Assay File Name', 'Study Assay Measurement Type', 'Study Assay Measurement Type Term Accession Number', 'Study Assay Measurement Type Term Source REF', 'Study Assay Technology Type', 'Study Assay Technology Type Term Accession Number', 'Study Assay Technology Type Term Source REF', 'Study Assay Technology Platform')

Collected header keys of STUDY ASSAYS section

altamisa.constants.investigation_headers.STUDY_PROTOCOL_NAME = 'Study Protocol Name'

altamisa.constants.investigation_headers.STUDY_PROTOCOL_TYPE = 'Study Protocol Type'

altamisa.constants.investigation_headers.STUDY_PROTOCOL_TYPE_TERM_ACCESSION_NUMBER = 'Study Protocol Type Term Accession Number'

altamisa.constants.investigation_headers.STUDY_PROTOCOL_TYPE_TERM_SOURCE_REF = 'Study Protocol Type Term Source REF'

altamisa.constants.investigation_headers.STUDY_PROTOCOL_DESCRIPTION = 'Study Protocol Description'

altamisa.constants.investigation_headers.STUDY_PROTOCOL_URI = 'Study Protocol URI'

altamisa.constants.investigation_headers.STUDY_PROTOCOL_VERSION = 'Study Protocol Version'

altamisa.constants.investigation_headers.STUDY_PROTOCOL_PARAMETERS_NAME = 'Study Protocol Parameters Name'

altamisa.constants.investigation_headers.STUDY_PROTOCOL_COMPONENTS_NAME = 'Study Protocol Components Name'

altamisa.constants.investigation_headers.STUDY_PROTOCOL_COMPONENTS_TYPE = 'Study Protocol Components Type'

altamisa.constants.investigation_headers.STUDY_PROTOCOLS_KEYS = ('Study Protocol Name', 'Study Protocol Type', 'Study Protocol Type Term Accession Number', 'Study Protocol Type Term Source REF', 'Study Protocol Description', 'Study Protocol URI', 'Study Protocol Version', 'Study Protocol Parameters Name', 'Study Protocol Parameters Name Term Accession Number', 'Study Protocol Parameters Name Term Source REF', 'Study Protocol Components Name', 'Study Protocol Components Type', 'Study Protocol Components Type Term Accession Number', 'Study Protocol Components Type Term Source REF')

Collected header keys of STUDY PROTOCOLS section

altamisa.constants.investigation_headers.STUDY_PERSON_LAST_NAME = 'Study Person Last Name'

altamisa.constants.investigation_headers.STUDY_PERSON_FIRST_NAME = 'Study Person First Name'

altamisa.constants.investigation_headers.STUDY_PERSON_MID_INITIALS = 'Study Person Mid Initials'

altamisa.constants.investigation_headers.STUDY_PERSON_EMAIL = 'Study Person Email'

altamisa.constants.investigation_headers.STUDY_PERSON_PHONE = 'Study Person Phone'

altamisa.constants.investigation_headers.STUDY_PERSON_FAX = 'Study Person Fax'

altamisa.constants.investigation_headers.STUDY_PERSON_ADDRESS = 'Study Person Address'

altamisa.constants.investigation_headers.STUDY_PERSON_AFFILIATION = 'Study Person Affiliation'

altamisa.constants.investigation_headers.STUDY_PERSON_ROLES = 'Study Person Roles'

altamisa.constants.investigation_headers.STUDY_PERSON_ROLES_TERM_ACCESSION_NUMBER = 'Study Person Roles Term Accession Number'

altamisa.constants.investigation_headers.STUDY_PERSON_ROLES_TERM_SOURCE_REF = 'Study Person Roles Term Source REF'

altamisa.constants.investigation_headers.STUDY_CONTACTS_KEYS = ('Study Person Last Name', 'Study Person First Name', 'Study Person Mid Initials', 'Study Person Email', 'Study Person Phone', 'Study Person Fax', 'Study Person Address', 'Study Person Affiliation', 'Study Person Roles', 'Study Person Roles Term Accession Number', 'Study Person Roles Term Source REF')

Collected header keys of STUDY CONTACTS section

Table Headers

Constants of valid column headers for study and assay table parsing and writing, as specified in the ISA-Tab study and assay specifications.

altamisa.constants.table_headers.EXTRACT_NAME = 'Extract Name'

altamisa.constants.table_headers.LABELED_EXTRACT_NAME = 'Labeled Extract Name'

altamisa.constants.table_headers.LIBRARY_NAME = 'Library Name'

Special material (see Special Extensions)

altamisa.constants.table_headers.SAMPLE_NAME = 'Sample Name'

altamisa.constants.table_headers.SOURCE_NAME = 'Source Name'

altamisa.constants.table_headers.ARRAY_DATA_FILE = 'Array Data File'

altamisa.constants.table_headers.ARRAY_DATA_MATRIX_FILE = 'Array Data Matrix File'

altamisa.constants.table_headers.ARRAY_DESIGN_FILE = 'Array Design File'

altamisa.constants.table_headers.DERIVED_ARRAY_DATA_FILE = 'Derived Array Data File'

altamisa.constants.table_headers.DERIVED_ARRAY_DATA_MATRIX_FILE = 'Derived Array Data Matrix File'

altamisa.constants.table_headers.DERIVED_DATA_FILE = 'Derived Data File'

altamisa.constants.table_headers.DERIVED_SPECTRAL_DATA_FILE = 'Derived Spectral Data File'

altamisa.constants.table_headers.IMAGE_FILE = 'Image File'

altamisa.constants.table_headers.METABOLITE_ASSIGNMENT_FILE = 'Metabolite Assignment File'

altamisa.constants.table_headers.PEPTIDE_ASSIGNMENT_FILE = 'Peptide Assignment File'

altamisa.constants.table_headers.PROTEIN_ASSIGNMENT_FILE = 'Protein Assignment File'

altamisa.constants.table_headers.RAW_DATA_FILE = 'Raw Data File'

altamisa.constants.table_headers.RAW_SPECTRAL_DATA_FILE = 'Raw Spectral Data File'

altamisa.constants.table_headers.SPOT_PICKING_FILE = 'Spot Picking File'

altamisa.constants.table_headers.ASSAY_NAME = 'Assay Name'

altamisa.constants.table_headers.DATA_TRANSFORMATION_NAME = 'Data Transformation Name'

altamisa.constants.table_headers.GEL_ELECTROPHORESIS_ASSAY_NAME = 'Gel Electrophoresis Assay Name'

altamisa.constants.table_headers.HYBRIDIZATION_ASSAY_NAME = 'Hybridization Assay Name'

altamisa.constants.table_headers.MS_ASSAY_NAME = 'MS Assay Name'

altamisa.constants.table_headers.NORMALIZATION_NAME = 'Normalization Name'

altamisa.constants.table_headers.PROTOCOL_REF = 'Protocol REF'

altamisa.constants.table_headers.SCAN_NAME = 'Scan Name'

altamisa.constants.table_headers.DATE = 'Date'

altamisa.constants.table_headers.LABEL = 'Label'

altamisa.constants.table_headers.MATERIAL_TYPE = 'Material Type'

altamisa.constants.table_headers.PERFORMER = 'Performer'

altamisa.constants.table_headers.TERM_SOURCE_REF = 'Term Source REF'

altamisa.constants.table_headers.TERM_ACCESSION_NUMBER = 'Term Accession Number'

altamisa.constants.table_headers.UNIT = 'Unit'

altamisa.constants.table_headers.ARRAY_DESIGN_REF = 'Array Design REF'

altamisa.constants.table_headers.FIRST_DIMENSION = 'First Dimension'

altamisa.constants.table_headers.SECOND_DIMENSION = 'Second Dimension'

altamisa.constants.table_headers.CHARACTERISTICS = 'Characteristics'

altamisa.constants.table_headers.COMMENT = 'Comment'

altamisa.constants.table_headers.FACTOR_VALUE = 'Factor Value'

altamisa.constants.table_headers.PARAMETER_VALUE = 'Parameter Value'

altamisa.constants.table_headers.DATA_FILE_HEADERS = ('Array Data File', 'Array Data Matrix File', 'Array Design File', 'Derived Array Data File', 'Derived Array Data Matrix File', 'Derived Data File', 'Derived Spectral Data File', 'Image File', 'Metabolite Assignment File', 'Peptide Assignment File', 'Post Translational Modification Assignment File', 'Protein Assignment File', 'Raw Data File', 'Raw Spectral Data File', 'Spot Picking File')

Collected header keys indicating a data file.

altamisa.constants.table_headers.MATERIAL_NAME_HEADERS = ('Extract Name', 'Labeled Extract Name', 'Library Name', 'Sample Name', 'Source Name', 'Array Data File', 'Array Data Matrix File', 'Array Design File', 'Derived Array Data File', 'Derived Array Data Matrix File', 'Derived Data File', 'Derived Spectral Data File', 'Image File', 'Metabolite Assignment File', 'Peptide Assignment File', 'Post Translational Modification Assignment File', 'Protein Assignment File', 'Raw Data File', 'Raw Spectral Data File', 'Spot Picking File')

Collected header keys indicating a material/data name.

altamisa.constants.table_headers.PROCESS_NAME_HEADERS = ('Assay Name', 'Data Transformation Name', 'Gel Electrophoresis Assay Name', 'Hybridization Assay Name', 'MS Assay Name', 'Normalization Name', 'Scan Name')

Collected header keys indicating a process name.

Table Restrictions

Constants used for validation of data and annotation restrictions in study and assay tables.

altamisa.constants.table_restrictions.PROTEIN_EXPRESSION_PROFILING = 'protein expression profiling'

altamisa.constants.table_restrictions.PROTEIN_IDENTIFICATION = 'protein identification'

altamisa.constants.table_restrictions.METABOLITE_PROFILING = 'metabolite profiling'

altamisa.constants.table_restrictions.DNA_MICROARRAY = 'dna microarray'

altamisa.constants.table_restrictions.GEL_ELECTROPHORESIS = 'gel electrophoresis'

altamisa.constants.table_restrictions.PROTEIN_MICROARRAY = 'protein microarray'

altamisa.constants.table_restrictions.NUCLEOTIDE_SEQUENCING = 'nucleotide sequencing'

altamisa.constants.table_restrictions.MASS_SPECTROMETRY = 'mass spectrometry'

altamisa.constants.table_restrictions.PT_DATA_COLLECTION = 'data collection'

altamisa.constants.table_restrictions.PT_DATA_NORMALIZATION = 'data normalization'

altamisa.constants.table_restrictions.PT_DATA_TRANSFORMATION = 'data transformation'

altamisa.constants.table_restrictions.PT_ELECTROPHORESIS = 'electrophoresis'

altamisa.constants.table_restrictions.PT_HYBRIDIZATION = 'hybridization'

altamisa.constants.table_restrictions.PT_MASS_SPECTROMETRY = 'mass spectrometry'

altamisa.constants.table_restrictions.PT_NUCLEIC_ACID_HYBRIDIZATION = 'nucleic acid hybridization'

altamisa.constants.table_restrictions.RESTRICTED_MATERIALS_ATECH = {'Library Name': {'nucleotide sequencing'}}

Materials restricted to certain assay technologies

altamisa.constants.table_restrictions.RESTRICTED_MATERIALS_AMEAS = {}

Materials restricted to certain assay measurements

altamisa.constants.table_restrictions.RESTRICTED_FILES_ATECH = {'Array Data File': {'dna microarray', 'protein microarray'}, 'Array Data Matrix File': {'dna microarray', 'protein microarray'}, 'Array Design File': {'dna microarray', 'protein microarray'}, 'Derived Array Data File': {'dna microarray', 'protein microarray'}, 'Derived Array Data Matrix File': {'dna microarray', 'protein microarray'}, 'Derived Spectral Data File': {'mass spectrometry'}, 'Metabolite Assignment File': {'mass spectrometry'}, 'Peptide Assignment File': {'mass spectrometry'}, 'Post Translational Modification Assignment File': {'mass spectrometry'}, 'Protein Assignment File': {'mass spectrometry'}, 'Raw Spectral Data File': {'mass spectrometry'}, 'Spot Picking File': {'gel electrophoresis'}}

Data files restricted to certain assay technologies

altamisa.constants.table_restrictions.RESTRICTED_FILES_AMEAS = {'Metabolite Assignment File': {'metabolite profiling'}, 'Peptide Assignment File': {'protein expression profiling', 'protein identification'}, 'Post Translational Modification Assignment File': {'protein expression profiling', 'protein identification'}, 'Protein Assignment File': {'protein expression profiling', 'protein identification'}}

Data files restricted to certain assay measurements

altamisa.constants.table_restrictions.RESTRICTED_PROTO_NAMES_ATECH = {'Gel Electrophoresis Assay Name': {'gel electrophoresis'}, 'Hybridization Assay Name': {'dna microarray', 'protein microarray'}, 'MS Assay Name': {'mass spectrometry'}, 'Scan Name': {'dna microarray', 'gel electrophoresis', 'protein microarray'}}

Protocol names restricted to certain assay technologies

altamisa.constants.table_restrictions.RESTRICTED_PROTO_NAMES_PTYPE = {'Data Transformation Name': {'data transformation'}, 'Gel Electrophoresis Assay Name': {'electrophoresis'}, 'Hybridization Assay Name': {'hybridization', 'nucleic acid hybridization'}, 'MS Assay Name': {'mass spectrometry'}, 'Normalization Name': {'data normalization'}, 'Scan Name': {'data collection'}}

Protocol names restricted by certain protocol types (ignored if ref is UNKNOWN)

altamisa.constants.table_restrictions.RESTRICTED_PROTO_ANNOS_ATECH = {'Array Design REF': {'dna microarray', 'protein microarray'}, 'First Dimension': {'gel electrophoresis'}, 'Second Dimension': {'gel electrophoresis'}}

Protocol special case annotations restricted to certain assay technologies

altamisa.constants.table_restrictions.RESTRICTED_PROTO_ANNOS_PTYPE = {'Array Design REF': {'hybridization', 'nucleic acid hybridization'}, 'First Dimension': {'electrophoresis'}, 'Second Dimension': {'electrophoresis'}}

Protocol special case annotations restricted to certain protocol types

Table Tokens

Token constants for study and assay table parsing and writing.

altamisa.constants.table_tokens.TOKEN_ANONYMOUS = 'Anonymous'

Used for marking anonymous/unnamed Processes

altamisa.constants.table_tokens.TOKEN_EMPTY = 'Empty'

Used for marking empty/unnamed Data

altamisa.constants.table_tokens.TOKEN_UNKNOWN = 'Unknown'

Used for named Processes without protocol reference