Commonly misused terms from RefGenomes Project

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• Regulates (examples: Emily:)
• activation versus positive regulation
• Response to (examples: Emily:)

• electron carrier activity (GO:0009055)

• development
• morphogenesis
• differentiation

• protein binding: this term is being used inconsistently.
• 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 cycle
• cell proliferation

• peptide secretion
• protein secretion

• gene expression, GO:0010467
• regulation of gene expression, GO:0010468
• regulation of transcription

• 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.

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