Misused terms

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Protein production as a readout for a biological process

  • Most annotations are either completely incorrect or refer to regulation of the process (ie, involvement is indirect)
  • Action for annotations may be (i) update annotation to regulation of x; (ii) update annotation to x protein/peptide production, (iii) update annotation annotation to a signaling pathway; or (iv) no action needed

Cytokine secretion

  • GO:0050707 regulation of cytokine secretion
  • GO:0050715 positive regulation of cytokine secretion
  • GO:0050710 negative regulation of cytokine secretion

and all children:

  • GO:1900040 regulation of interleukin-2 secretion
  • GO:2001179 regulation of interleukin-10 secretion

GO:0030073 insulin secretion

42 proteins directly annotated

  1. EVALUATE Manual annotations to insulin secretion and children
  2. EVALUATE Protein secretion

GO:0002790 : peptide secretion

3 annotations; might be correct ? if correct - document as example cases


GO:0002776 : antimicrobial peptide secretion

1 annotation: Q10738 Mmp7 - mouse


GO:0002782 antifungal peptide secretion

4 annotations: P14661 ASCEC-1, Q5H7N6 ASCEC-2, Q5H7N5 ASCEC-3, Q5H7N4 ASCEC-4


GO:0051458 : corticotropin secretion

1 annotation Aqp1 mouse


GO:0030252 : growth hormone secretion

33 gene products annotated; looks like most should be moved to regulation of the process


GO:0030072 : peptide hormone secretion

(insulin secretion already covered above)


GO:0034645 : cellular macromolecule biosynthetic process and children

The concept of "protein biosynthetic process" is inconsistent with other terms in the ontology: protein production is also described by "translation" and by "protein production". The parent term "biosynthetic process" is defined as "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." Proteins are produced by a more specific type of this process, translation.

Cellular macromolecule metabolic process & children

  1. GO:0042967 : acyl-carrier-protein biosynthetic process [0 gene products]
    • Suggestion: DELETE
  2. GO:0070589 : cellular component macromolecule biosynthetic process [1582 gene products]
    1. GO:0031506 : cell wall glycoprotein biosynthetic process [91 gene products]
  3. GO:0033692 : cellular polysaccharide biosynthetic process [2714 gene products]
    • legitimate cellular macromolecule biosynthetic process
  4. GO:0071897 : DNA biosynthetic process [447 gene products]
    • To investigate
  5. GO:0006260 : DNA replication [6640 gene products]
    • legitimate cellular macromolecule biosynthetic process
  6. GO:0043172 : ferredoxin biosynthetic process [0 gene products]
    • Suggestion: DELETE
  7. GO:0042965 : glutaredoxin biosynthetic process [1 gene product]
    • Suggestion: DELETE
  8. GO:0009101 : glycoprotein biosynthetic process [3034 gene products]
  9. GO:0042541 : hemoglobin biosynthetic process [82 gene products, including 17 EXP annotations]
  10. GO:0042158 : lipoprotein biosynthetic process [1114 gene products]
  11. GO:2000113 : negative regulation of cellular macromolecule biosynthetic process [9835 gene products]
  12. GO:0070501 : poly-gamma-glutamate biosynthetic process [0 gene products]
    • Suggestion: DELETE
  13. GO:2000112 : regulation of cellular macromolecule biosynthetic process [39860 gene products]
  14. GO:0042964 : thioredoxin biosynthetic process [2 gene products]
    • Suggestion: DELETE
  15. GO:0006351 : transcription, DNA-dependent [40985 gene products]
  16. GO:0006412 : translation [26294 gene products]
    • legitimate cellular macromolecule biosynthetic process
  17. GO:0006414 : translational elongation [3903 gene products]
    • Should this not be part of GO:0006412 translation ?


gene expression, GO:0010467

regulation of gene expression, GO:0010468

regulation of transcription

Others

protein homoligomerization activity, and all related processes

Can use term 'protein complex assembly' if we define a complex as two or more polypeptides like in http://en.wikipedia.org/wiki/Multiprotein_complex

===Regulates; activation versus positive regulation

Response to

electron carrier activity (GO:0009055)

development, morphogenesis, differentiation

protein binding

  • X protein binding: should not be used in conjunction with X complex term: if a protein is a member of that complex, it does not bind it. However not all experiments allow to distinguish that.

SQL query to find those: SELECT distinct gene_product.symbol AS g_symbol, gene_product.full_name AS gp_full_name, dbxref.xref_dbname AS gp_dbname, dbxref.xref_key AS gp_acc, species.genus, species.species, species.common_name FROM term AS t1 INNER JOIN graph_path AS cl1 ON (t1.id=cl1.term1_id) INNER JOIN association AS a1 ON (cl1.term2_id=a1.term_id) INNER JOIN gene_product ON (a1.gene_product_id=gene_product.id) INNER JOIN species ON (gene_product.species_id=species.id) INNER JOIN dbxref ON (gene_product.dbxref_id=dbxref.id) INNER JOIN association AS a2 ON (a2.gene_product_id=gene_product.id) INNER JOIN graph_path AS cl2 ON (a2.term_id=cl2.term2_id) INNER JOIN term AS t2 ON (cl2.term1_id=t2.id) INNER JOIN evidence AS ev1 ON (a1.id=ev1.association_id) INNER JOIN evidence AS ev2 ON (a2.id=ev2.association_id) WHERE t1.name = 'protein binding' AND t2.name = 'protein complex' AND a1.is_not=0 AND genus='Dictyostelium' AND ev1.code <> 'IEA' AND ev2.code <> 'IEA' AND cl1.term2_id <> t1.id


growth, cell growth, cell proliferation

cell cycle and cell proliferation

  • protein carrier activity (Val Wood): The old term "protein carrier activity" had a definition whcih made it a transmembrane transporter "Catalysis of the transfer of proteins from one side of a membrane to the other" which made it a transmembrane transporter so it was renamed "protein transmembrane transporter activity". Quite a few of us have used the old term to annotate karyopherins (which was incorrect as the nucler membrane (i.e lipid bilayer) is not penetrated during transport through the nuclear pore). These need moving to protein transporter activity; GOid=GO:0008565.

TASK X Cell cycle terms

  • We will look at that once the reorganization of the cell cycle terms is finished (aim: Fall 2013)

Resolved

  • 'part' terms: do we use them or not? YES WE CAN USE THEM


  • OBSOLETED: electron transport (GO:0006118)
  • GO TERM COMMENTED pseudouridylate synthase activity (GO:0004730) (Val Wood):"Note that this term should not be confused with 'pseudouridine synthase activity ; GO:0009982', which refers to the intramolecular isomerization of uridine to pseudouridine." should be abbotated to pseudouridine synthase activity GO:0009982 or its child

tRNA-pseudouridine synthase activity (The SGD annotation that a number of groups ISS'd to was updated yesterday).

  • OBSOLETED: secretory pathway (GO:00450055): ONly terms involved in the secretory machinery should be annotated. Currently, many secreted proteins are annotated (March 12-2008):

- ZFIN: cxcl12a (chemokine) - Rice: Alpha-galactosidase precursor - human NMUR1