Class: pombase phaf association

line of PHAF

URI: ontology_association:PombasePhafAssociation

Parents

• is_a: Association - generic association between an entity and an ontological term

Uses Mixin

• mixin: Denormalized - mixin for a denormalized class. A denormalized class is formed from a join of two or more other classes

Referenced by Class

• PombasePhafAssociationDocument pombase phaf association document➞associations _0..* PombasePhafAssociation

Attributes

Own

• Database name _1..1
  • Description: The database that produced the file – included to facilitate data sharing with other databases. Obviously always PomBase for this file.
  • Range: Database_name_enum
  • Example: PomBase None
• Gene systematic ID _1..1
  • Description: The systematic ID for each gene.
  • Range: String
  • Example: SPBC1773.02c None
• FYPO ID _1..1
  • Description: To use the FYPO IDs, see the FYPO summary page and the FAQ on browsing FYPO.
  • Range: FYPOIdentifier
  • Example: FYPO:0001164 None
• Allele description _0..1
  • Description: The allele description specifically describes the change; see the Phenotype data bulk upload format for details on allele types and descriptions.
  • Range: String
  • Example: G126D None
• Expression _0..1
  • Description: The Expression column contains one of these values: ‘overexpression’, ‘knockdown’, ‘endogenous’, ‘null’, ‘not specified’. Deletions always have ‘null’ expression.
  • Range: Expression_enum
  • Example: Overexpression None
• Parental strain _0..1
  • Description: The Parental strain column is for the parental strain designation, such as 972 h-, 975 h+, etc. This column must be filled in, but “unknown” is allowed.
  • Range: String
  • Example: 972 h- None
• Strain name (background) _0..1
  • Description: The Background strain name column is used for a lab’s in-house name/ID/designation for the background strain (i.e. the derivative of the parental strain that has selectable marker alleles etc.). The description in the Genotype column should match this background strain.
  • Range: String
• Genotype description _0..1
  • Description: The Background genotype description column is for alleles in the background, such as selectable markers; these details are optional. To avoid redundancy, it does not repeat the allele of interest (from column 4 or 10) in the genotype column.
  • Range: String
• Gene name _0..1
  • Description: Gene names are optional for upload, but are included where available in the download.
  • Range: String
  • Example: bcp1 None
• Allele name _0..1
  • Description: Allele names are optional for upload, but are included where available in the download. Column 10 lists the preferred allele name, and any alternative names are in column 11.
  • Range: String
  • Example: bcp1+ None
• Allele synonym _0..1
  • Description: See note on Allele name above. Multiple entries are separated with pipes (|).
  • Range: String
• Allele type _0..1
  • Description: Allowed allele types, example descriptions, etc. are shown in the table at the bottom of the Phenotype data bulk upload format page.
  • Range: Allele_type_enum
  • Example: wild_type None
• Evidence _1..1
  • Description: For the Evidence column, we use a small selection from the Evidence Ontology (ECO). Please contact the Helpdesk if you need assistance using these IDs
  • Range: Evidence_enum
  • Example: cell growth assay evidence None
• Condition _0..1
  • Description: Conditions use a small ontology maintained in-house by PomBase curators, and we can help you interpret the IDs. Multiple entries are shown in cases where more than one condition detail applies at the same time (e.g. high temperature, minimal medium), and are separated with commas (,).
  • Range: PECOIdentifier
  • Example: PECO:0000126,PECO:0000102 None
• Penetrance _0..1
  • Description: Penetrance describes the proportion of a population that shows a cell-level phenotype. Penetrance data are represented as percents or entries from the in-house FYPO_EXT ontology (FYPO_EXT:0000001 = high; FYPO_EXT:0000002 = medium; FYPO_EXT:0000003 = low; FYPO_EXT:0000004 = full).
  • Range: String
  • Example: FYPO_EXT:0000002 None
• Severity _0..1
  • Description: Severity (formerly designated “expressivity”) uses the FYPO_EXT ontology described in description of Penetrance
  • Range: FYPOEXTIdentifier
  • Example: FYPO_EXT:0000001 None
• Extension _0..*
  • Description: The Extension column is used to record when a mutation in one gene affects another gene or its product. For example, if a mutation in gene A decreases its ability to phosphorylate protein B, the A allele is annotated to the phenotype “decreased protein kinase activity” with the ID for gene B in an extension. In the downloadable file, an annotation can have multiple comma-separated extensions if they combine to form a “compound” extension (e.g. two or more genes assayed together).
  • Range: String
  • Example: assayed_using(PomBase:SPBC11B10.09) None
• Reference _1..*
  • Description: The Reference column has the publication’s PubMed ID (PMID).
  • Range: Publication
  • Example: PMID:19229492 None
• Taxon _1..1
  • Description: The taxon will usually be 4896 (the NCBI taxon ID for Schizosaccharomyces pombe), although an NCBI taxon ID for a specific S. pombe strain would be allowed.
  • Range: Integer
  • Example: 4896 None
• Date _0..1
  • Description: The date is the date on which the annotations are created. Format: YYYY-MM-DD
  • Range: String
  • Example: 20141023 None