Function terms to be obsoleted

[gocentral]

Here is another list of terms for obsoletion. Most are gene products. We aim to take these out of the ontology before the term names are changed on March 5th. Please check the list and post any objections.

The terms following the arrow (-->) are those to which annotation should be made.

GO:0005106 ephrin GO:0005107 GPI-linked ephrin GO:0005108 transmembrane ephrin ephrin plus children: class of proteins that interact with the ephrin receptors. --> ephrin receptor binding ; GO:0046new integral to plasma membrane ; GO:0005887 (for transmembrane ephrin) extrinsic to plasma membrane ; GO:0019897 (for GPI-linked ephrin)

GO:0005177 neuroligin One class of ligands for specific neurexins has been identified as Neuroligin-1, Neuroligin-2, and Neuroligin-3, neuronal cell surface proteins arising by alternative splicing, found in synaptic plasma membranes, and expressed at high levels only in brain. The three proteins bind to splice variants of Beta-Neurexins lacking a certain insert but not if they contain this insert. --> neurexin binding ; GO:0042043

GO:0015053 opsin GO:0015059 blue-sensitive opsin GO:0015060 green-sensitive opsin GO:0015061 red-sensitive opsin GO:0015062 violet-sensitive opsin GO:0015063 long-wave-sensitive opsin GO:0015064 UV-sensitive opsin GO:0016016 short-wave-sensitive opsin glycoprotein from visual pigment. combines with 11-cis-retinal or 3,4-didehydro-11-cis-retinal -->retinal binding ; GO:0016918 -OR- 3,4-didehydroretinal binding ; GO:0046new Will check whether the specific terms can be annotated to specific retinal isomers

GO:0001524 globin GO:0016969 hemerythrin GO:0016970 hemocyanin --> oxygen transporter ; GO:0005344

GO:0003772 co-chaperonin Chaperonin = Subset of chaperone proteins found in prokaryotes, mitochondria and plastids major example is prokaryotic GroEL -->co-chaperone ; GO:0003767 Can someone define co-chaperone? I'm not sure that it's a true function.

GO:0004868 serpin A protein family -->serine protease inhibitor ; GO:0004867

GO:0008100 lipophorin Any member of the major class of lipid-transporting proteins found in the hemolymph of insects. -->lipid transporter ; GO:0005319

GO:0008648 tachykinin pharmacologically, they all cause hypotension [pathological] in mammals, contraction of gut and bladder smooth muscle, and secretion of saliva. (online med dict) a family of hormones that are potent, rapidly acting secretagogues and cause smooth muscle contraction and vasodilation (dorlands) rapid stimulant effect on vascular and non-vascular muscle. stimulate salivary and lachrymal secretion (bible) -->positive regulation of saliva secretion ; GO:0046new positive regulation of smooth muscle contraction ; GO:0045987 positive regulation of vasodilation ;GO:0045909

GO:0009457 flavodoxin -->electron transporter ; GO:005489

GO:0016086 allatostatin Peptide hormones produced by the corpora allata of insects that reversibly inhibit the production of juvenile hormone. -->negative regulation of juvenile hormone biosynthesis ; GO:0045968

GO:0016088 insulin stimulates glucose uptake by muscle and adipose tissue, promotes glycogenesis, lipogenesis, synthesis of proteins and nucleic acid -->positive regulation of glucose import ; GO:0046326 positive regulation of gluconeogenesis ; GO:0045722 positive regulation of protein biosynthesis ; GO:0045727 positive regulation of nucleic acid biosynthesis ; GO:0046new

GO:0016541 intein Intervening protein sequence excised from a protein precursor in protein splicing; inteins catalyze their own excision and many also possess endonuclease activity. -->endonuclease ; GO:0004519

GO:0016915 activin Stimulates the secretion of follicle-stimulating hormone. (Dorlands/bible) -->positive regulation of follicle-stimulating hormone secretion ; GO:0046new

GO:0016916 inhibin Opposite effects to activin -->negative regulation of follicle-stimulating hormone secretion ; GO:0046new

GO:0016975 alpha-2 macroglobulin Inhibition of proteinase by a mechanism involving a bait region which contains specific sites, cleavage of which induces a conformational change that results in trapping of the proteinase; following cleavage in the bait region a thiolester bond is hydrolyzed and mediates the covalent binding of the protein to the proteinase; subsequently epsilon-amino groups of the proteinase react with thiolester linkages in the inhibitor to form stable amide links; the entrapped proteinase can now only act on low molecular mass substrates. -->endopeptidase inhibitor ; GO:0004866

GO:0017043 adrenocorticotropin ( = corticotrophin) stimulates growth of adrenal cortex, synthesis and secretion of various corticosteroids (bible) It stimulates the adrenal cortex to secrete glucocorticoid hormones (online med dict) -->regulation of hormone secretion ; GO:0046new

GO:0015480 secretin (sensu Bacteria) Secretins are Gram-negative bacterial outer membrane proteins that form multimeric pores through which macromolecules, usually proteins, can pass. Form homomultimeric ring structures, 10-20 subunits per complex, with large central pores (inner diameters of 5-10 nm). -->integral to external outer membrane (sensu Gram-negative Bacteria) ; GO:0045203 protein transporter ; GO:0008565

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/685":https://sourceforge.net/p/geneontology/ontology-requests/685

[gocentral]

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Will we retain the obsolete terms as synonyms anywhere?

Original comment by: jl242

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In the easy cases where the gene product is an example of the terms suggested as alternatives (eg. serpin, lipophorin), yep. Where the gene product has lots of functions (eg. insulin), no.

Original comment by: girlwithglasses

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Amendment to intein entry: GO:0016541 intein Intervening protein sequence excised from a protein precursor in protein splicing; inteins catalyze their own excision and many also possess endonuclease activity. -->endonuclease ; GO:0004519 protein splicing ; GO:0016539

Original comment by: girlwithglasses

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There are 2 that I wonder about. 1) Can't neuroligan simply be merged with neurexin binding based on its definition? 2) The different types of opsins have vey different functions in that they are stimulated by different wavelengths of light. This has very important implications in the field of visual research.

In general, I think terms should only be obsoleted as a last resort. Whenever possible, if the concept is useful, then we should either try to rename terms or merge them with other terms. Otherwise the obsolete node will beome unmanageable and we will probably end up reinstantiating concepts that were originally obsoleted. For example, useful terms that contain cellular details and functional details may some day be reborn using slots. I think it will be a lot easier to keep those terms for now and then create equivalencies for them later than to try to resurrect the concepts at some point in the future (which will create confusion in the long run).

Original comment by: ukemi

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Once GO moves over to the database format, the size of the obsolete node won't matter - obsolete will just become a database tag. The reason for obsoleting these terms is because they aren't valid functions - they're gene products or classes of proteins. You can't say that something has the function 'opsin' like you could say that it has the function 'protein binding' or a certain enzyme activity.

Re: the different types of opsins, I am researching whether they can be annotated to specific types of retinal binding (as stated above). If you have more information on this, please let me know. My aim is to replace these gene products with valid function terms without any loss of information. I am happy to postpone the obsoletion of opsin for the time being if you want to discuss this further, but I think opsin will need to be made obsolete as it is a class of proteins.

Original comment by: girlwithglasses

[gocentral]

Obsolete terms and comments

Original comment by: girlwithglasses

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All terms obsoleted EXCEPT co-chaperonin, which Rama is going to deal with. See attached document for the full comments added for each obsoleted term. In most cases I added a short definition for undefined terms.

Original comment by: girlwithglasses

[gocentral]

• status: open --> closed-fixed

Original comment by: girlwithglasses

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I would think that the "GO:0016088 insulin" could also be annotated to "hormone"., as would GO:0017043 adrenocorticotropin. I'm also wondering if the "opsin" terms could be reannoted to a G-coupled protein receptor (since it's the protein part of the rhdopsin).?

Original comment by: hdrabkin

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The main reason why I didn't suggest those terms as alternatives is that they are on my hitlist for obsoletion too! "Hormone" isn't a true activity, it's a class of molecules with a characteristic set of functions (mostly regulatory). I'm also dubious as to whether "G-coupled protein receptor" is really a function or whether it just describes the mode of downstream signaling that the receptor is involved in (which could be captured by a process term).

Original comment by: girlwithglasses

[gocentral]

• priority: 6 --> 5

Original comment by: mah11