Signaling Meeting Minutes January 2010

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5th January 2010

Participants: Alex Diehl, Peter D'Eustachio, Jennifer Deegan, Sandra Orchard, Susan Tweedie.

Discussion

  • We looked through the previously undefined terms and refined the definitions that Jennifer had made and added some new ones. The remaining undefined terms are modular and Jennifer will add definitions during the week.
  • Standard definitions

- is_a descendents of signaling process should be defined "The entirety of the process..."
- is_a descendents of signaling pathway terms should be defined "The series of molecular events whereby information is sent from [a] to [b]."

  • We discussed the meaning of "Termination":

Peter explained that there is a difference between the step when an instruction is given for the termination of a process, and that actual termination. An analogy is the delay between pressing the off switch on a computer and the end of the shut down proceedure. Peter pointed out that annotators may wish to annotate both of these points but that the control point when the order is given to terminate the process may be the more commonly used step.

Action items:

  • Jennifer will define the remaining undefined terms and fix the ids. She will then send a list of all the new terms that we have made to the participants, and send a link to the graph. The participants will double check what we have done.
  • Jennifer will write some documentation on what we have done to help future editors to follow our model.
  • We will meet again next monday at 4pm GMT and if all is well we will send our proposed graph to the GO list for comment, with an aim of committing to the live graph a few weeks later.

7th January

I have defined all the terms now. I am trying to extract a list of all the terms that we have made. It looks as if the branch was last taken on April the 6th so I am doing diffs from April 7th 2009.

The list of new terms that we have made is pasted below for reference:

[Term] id: ID:0000000 name: initiation of signal transduction namespace: biological_process def: "The process whereby a signal causes activation of a receptor, for example, via a conformation change. Gene products participating in this process include both ligands and receptors." [GOC:mtg_sig] comment: Note that this term is intended for the annotation of both ligands and receptors. is_a: ID:0000012 ! signaling process relationship: part_of GO:0007165 ! signal transduction created_by: jdeegan creation_date: 2009-03-23T10:03:58Z

[Term] id: ID:0000002 name: signal initiation by light namespace: biological_process def: "The process whereby a light signal causes activation of a receptor." [GOC:mtg_signal] is_a: ID:0000000 ! initiation of signal transduction created_by: jdeegan creation_date: 2009-03-23T10:04:36Z

[Term] id: ID:0000003 name: signal initiation by diffusible mediator namespace: biological_process def: "The process whereby a diffusible signal causes activation of a receptor." [GOC:mtg_signal] is_a: ID:0000000 ! initiation of signal transduction created_by: jdeegan creation_date: 2009-03-23T10:04:52Z

[Term] id: ID:0000004 name: signal initiation by physical damage namespace: biological_process def: "The process whereby a physical damage signal causes activation of a receptor." [GOC:mtg_signal] is_a: ID:0000019 ! signal initiation by mechanical effect created_by: jdeegan creation_date: 2009-03-23T10:05:05Z

[Term] id: ID:0000006 name: signaling via ionic flux namespace: biological_process def: "The process whereby information is sent from one location to another, within a living organism or between living organisms, via ionic flux." [GOC:mtg_signal] is_a: GO:0023017 ! signal transmission via diffusible molecule created_by: jdeegan creation_date: 2009-03-23T10:05:52Z

[Term] id: ID:0000007 name: neuronal signal transduction namespace: biological_process def: "The process whereby an activated neuronal cell receptor conveys information down a signaling pathway, resulting in a change in the function or state of a cell. This process may be intracellular or intercellular." [GOC:mtg_signal] is_a: GO:0007165 ! signal transduction is_a: ID:0000006 ! signaling via ionic flux created_by: jdeegan creation_date: 2009-03-23T10:06:12Z

[Term] id: ID:0000008 name: signaling via protein/peptide mediator namespace: biological_process def: "The process whereby information is sent from one location to another, within a living organism or between living organisms, via a protein/peptide mediator." [GOC:mtg_signal] is_a: GO:0023017 ! signal transmission via diffusible molecule created_by: jdeegan creation_date: 2009-03-23T10:06:27Z

[Term] id: ID:0000009 name: signaling via lipid mediator namespace: biological_process def: "The process whereby information is sent from one location to another, within a living organism or between living organisms, via a lipid mediator." [GOC:mtg_signal] is_a: GO:0023017 ! signal transmission via diffusible molecule created_by: jdeegan creation_date: 2009-03-23T10:06:52Z

[Term] id: ID:0000010 name: signaling via chemical mediator namespace: biological_process def: "The process whereby information is sent from one location to another, within a living organism or between living organisms, via a chemical mediator." [GOC:mtg_signal] is_a: GO:0023017 ! signal transmission via diffusible molecule created_by: jdeegan creation_date: 2009-03-23T10:07:13Z

[Term] id: ID:0000011 name: signal transmission via conformational transition namespace: biological_process def: "The process whereby a signal is conveyed via a conformational transition." [GOC:mtg_signal] relationship: part_of ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-04-06T02:08:10Z

[Term] id: ID:0000012 name: signaling process namespace: biological_process def: "Any biological process involved in the generation, transmission, reception, or interpretation of a signal. A signal is an entity used to transmit or convey information." [GOC:mtg_signaling] is_a: GO:0008150 ! biological_process relationship: part_of ID:0000018 ! signaling created_by: Jennifer I Deegan creation_date: 2009-04-06T02:22:22Z

[Term] id: ID:0000013 name: signal initiation by chemical mediator namespace: biological_process def: "The process whereby a chemical signal causes activation of a receptor." [GOC:mtg_signal] is_a: ID:0000003 ! signal initiation by diffusible mediator created_by: Jennifer I Deegan creation_date: 2009-04-06T02:31:23Z

[Term] id: ID:0000014 name: signal initiation by lipid mediator namespace: biological_process def: "The process whereby a lipid signal causes activation of a receptor." [GOC:mtg_signal] is_a: ID:0000003 ! signal initiation by diffusible mediator created_by: Jennifer I Deegan creation_date: 2009-04-06T02:32:08Z

[Term] id: ID:0000015 name: signal initiation by protein/peptide mediator namespace: biological_process def: "The process whereby a protein/peptide signal causes activation of a receptor." [GOC:mtg_signal] is_a: ID:0000003 ! signal initiation by diffusible mediator created_by: Jennifer I Deegan creation_date: 2009-04-06T02:32:27Z

[Term] id: ID:0000016 name: consequence of signal transmission namespace: biological_process def: "The steps whereby the downstream processes started by a signal are brought to a conclusion. For example destruction of cAMP by PDE, or endocytosis resulting from receptor phosphorylation. Most or all examples of this process are regulation steps. The termination process ends when the receptor has returned to its inactive state." [GOC:mtg_signaling] synonym: "signal termination" EXACT [] relationship: part_of ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-07-13T04:14:59Z

[Term] id: ID:0000017 name: regulation of signaling process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a signaling process." [GOC:mtg_signal] is_a: ID:0000012 ! signaling process created_by: Jennifer I Deegan creation_date: 2009-07-20T04:51:09Z

[Term] id: ID:0000018 name: signaling namespace: biological_process def: "The entirety of the process whereby information is transmitted. This process begins with the initiation of the signal and ends when a response has been triggered." [GOC:mtg_signaling] comment: The synthesis of the signal is not, in general, considered to be part of this process, but in some cases it is. Synthesis of insulin is not considered to be part of the insulin signaling pathway, and the insulin is assumed to have been made before the signaling process starts. is_a: GO:0008150 ! biological_process created_by: Jennifer I Deegan creation_date: 2009-07-13T04:24:06Z

[Term] id: ID:0000019 name: signal initiation by mechanical effect namespace: biological_process def: "The process whereby a mechanical signal causes activation of a receptor." [GOC:mtg_signal] is_a: ID:0000000 ! initiation of signal transduction created_by: Jennifer I Deegan creation_date: 2009-07-13T04:29:31Z

[Term] id: ID:0000020 name: signal initiation by stretch effect namespace: biological_process def: "The process whereby a stretch signal causes activation of a receptor." [GOC:mtg_signal] is_a: ID:0000019 ! signal initiation by mechanical effect created_by: Jennifer I Deegan creation_date: 2009-07-13T04:30:50Z

[Term] id: ID:0000021 name: signal initiation by peptide hormone namespace: biological_process def: "The process whereby a signal is initiated by a hormone (circular!). Note: an annotation of insulin could be made to this term. The process starts with the arrival of insulin and finishes ...\n\nThe membrane-bound components of the receptor including the ligand and receptor can all be annotated to this.\n\nWe should then break down by class in child terms. e.g. G-protein bound." [GOC:signaling] is_a: ID:0000015 ! signal initiation by protein/peptide mediator created_by: Jennifer I Deegan creation_date: 2009-07-13T04:36:37Z

[Term] id: ID:0000022 name: positive regulation of signaling process namespace: biological_process def: "Any process that activates, maintains or increases the frequency, rate or extent of a signaling process." [GOC:mtg_signal] is_a: ID:0000017 ! regulation of signaling process created_by: Jennifer I Deegan creation_date: 2009-07-20T04:51:26Z

[Term] id: ID:0000023 name: negative regulation of signaling process namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of a signaling process." [GOC:mtg_signal] is_a: ID:0000017 ! regulation of signaling process created_by: Jennifer I Deegan creation_date: 2009-07-20T04:51:56Z

[Term] id: ID:0000025 name: adaptation of signaling pathway namespace: biological_process def: "The regulation of a signal transduction pathway in response to a stimulus upon prolonged exposure to that stimulus." [GOC:mtg_sig] is_a: GO:0009966 ! regulation of signal transduction created_by: Jennifer I Deegan creation_date: 2009-08-03T04:13:01Z

[Term] id: ID:0000026 name: positive adaptation of signaling pathway namespace: biological_process def: "The positive regulation of a signal transduction pathway in response to a stimulus upon prolonged exposure to that stimulus." [GOC:mtg_sig] is_a: ID:0000022 ! positive regulation of signaling process is_a: ID:0000025 ! adaptation of signaling pathway created_by: Jennifer I Deegan creation_date: 2009-08-03T04:13:50Z

[Term] id: ID:0000027 name: signal transmission namespace: biological_process def: "The process whereby a signal is released and/or conveyed from one location to another. The process terminates at the end of the sub-process of signal transduction, when the function of the cell has been altered as a consequence of receipt of the signal." [GOC:mtg_signal] is_a: ID:0000012 ! signaling process created_by: Jennifer I Deegan creation_date: 2009-09-02T04:15:57Z

[Term] id: ID:0000028 name: signal release namespace: biological_process def: "The process whereby a signal is secreted or discharged into the extracellular medium from a cellular source." [GOC:mtg_signaling] is_a: ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:37:21Z

[Term] id: ID:0000029 name: signal transmission via transcytosis namespace: biological_process def: "The process whereby a signal is conveyed via transcytosis." [GOC:mtg_signal] is_a: ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:37:35Z

[Term] id: ID:0000030 name: signal transmission across a synapse namespace: biological_process def: "The process whereby a signal is conveyed across a synapse." [GOC:mtg_signal] is_a: ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:37:55Z

[Term] id: ID:0000031 name: signal transmission along a neuron namespace: biological_process def: "The process whereby a signal is conveyed along a neuron." [GOC:mtg_signal] is_a: ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:38:21Z

[Term] id: ID:0000032 name: signal transmission via blood namespace: biological_process def: "The process whereby a signal is conveyed via blood." [GOC:mtg_signal] is_a: ID:0000033 ! signal transmission via vascular system created_by: Jennifer I Deegan creation_date: 2009-09-02T04:40:22Z

[Term] id: ID:0000033 name: signal transmission via vascular system namespace: biological_process def: "The process whereby a signal is conveyed via the vascular system." [GOC:mtg_signal] is_a: ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:41:09Z

[Term] id: ID:0000034 name: signal transmission via lymphatic system namespace: biological_process def: "The process whereby a signal is conveyed via the lymphatic system." [GOC:mtg_signal] is_a: ID:0000033 ! signal transmission via vascular system created_by: Jennifer I Deegan creation_date: 2009-09-02T04:41:51Z

[Term] id: ID:0000035 name: signal transmission via phloem namespace: biological_process def: "The process whereby a signal is conveyed via the phloem." [GOC:mtg_signal] is_a: ID:0000033 ! signal transmission via vascular system created_by: Jennifer I Deegan creation_date: 2009-09-02T04:42:27Z

[Term] id: ID:0000036 name: signal transmission via xylem namespace: biological_process def: "The process whereby a signal is conveyed via the xylem." [GOC:mtg_signal] is_a: ID:0000033 ! signal transmission via vascular system created_by: Jennifer I Deegan creation_date: 2009-09-02T04:42:45Z

[Term] id: ID:0000037 name: signal transmission via air namespace: biological_process def: "The process whereby a signal is conveyed via the air." [GOC:mtg_signal] is_a: ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:49:19Z

[Term] id: GO:0055125 name: behavioral signaling namespace: biological_process def: "The entirety of the behavioral process whereby information is sent between living organisms." [GOC:mtg_signal] is_a: ID:0000018 ! signaling created_by: Jennifer I Deegan creation_date: 2009-10-28T04:21:32Z

[Term] id: GO:0055126 name: signaling pathway namespace: biological_process def: "The series of molecular events whereby information is sent from one location to another within a living organism or between living organisms." [GOC:mtg_signal] is_a: ID:0000018 ! signaling created_by: Jennifer I Deegan creation_date: 2009-10-28T04:21:54Z

[Term] id: GO:0055127 name: intracellular signaling pathway namespace: biological_process alt_id: GO:0055128 def: "The series of molecular events whereby information is sent from one location to another within a living organism." [GOC:mtg_signal] synonym: "intercellular signaling" EXACT [] synonym: "intracellular signal transduction pathway" RELATED [] is_a: GO:0055126 ! signaling pathway created_by: Jennifer I Deegan creation_date: 2009-10-28T04:27:25Z

[Term] id: GO:0055129 name: CD40 signaling pathway namespace: biological_process def: "Any series of molecular signals generated as a consequence of binding to the receptor CD40." [GOC:sig] is_a: GO:0055127 ! intracellular signaling pathway created_by: Jennifer I Deegan creation_date: 2009-10-28T04:44:32Z

[Term] id: GO:0023004 name: activation of dopamine receptor signaling pathway namespace: biological_process def: "Any process that initiates the dopamine receptor protein signaling pathway through stimulation of the dopamine receptor." [GOC:mtg_signaling] synonym: "initiation of dopamine receptor signaling pathway" RELATED [] synonym: "stimulation of dopamine receptor signaling pathway" EXACT [] is_a: GO:0023005 ! signal initiation by neurotransmitter is_a: GO:0060161 ! positive regulation of dopamine receptor signaling pathway created_by: Jennifer I Deegan creation_date: 2009-11-23T04:28:24Z

[Term] id: GO:0023005 name: signal initiation by neurotransmitter namespace: biological_process def: "The process whereby a neurotransmitter signal causes activation of a receptor." [GOC:mtg_signal] is_a: ID:0000003 ! signal initiation by diffusible mediator created_by: Jennifer I Deegan creation_date: 2009-11-23T04:34:34Z

[Term] id: GO:0023006 name: signal initiation by amino acid namespace: biological_process def: "The process whereby an amino acid signal causes activation of a receptor." [GOC:mtg_signal] is_a: ID:0000003 ! signal initiation by diffusible mediator created_by: Jennifer I Deegan creation_date: 2009-11-23T04:35:16Z

[Term] id: GO:0023007 name: ligand binding to T cell receptor namespace: biological_process def: "(initiation)" [GOC:jid] is_a: GO:0050862 ! positive regulation of T cell receptor signaling pathway created_by: Jennifer I Deegan creation_date: 2009-11-30T04:42:10Z

[Term] id: GO:0023009 name: initiation of T cell receptor signaling namespace: biological_process def: "The process whereby a signal causes activation of T cell receptor signaling." [GOC:mtg_signal] is_a: ID:0000015 ! signal initiation by protein/peptide mediator created_by: Jennifer I Deegan creation_date: 2009-12-02T11:07:14Z

[Term] id: GO:0023010 name: regulation of initiation of T cell receptor signaling namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the initiation of T cell receptor signaling." [GOC:mtg_signal] is_a: GO:0023009 ! initiation of T cell receptor signaling created_by: Jennifer I Deegan creation_date: 2009-12-02T11:08:13Z

[Term] id: GO:0023011 name: positive regulation of initiation of T cell receptor signaling namespace: biological_process def: "Any process that activates, maintains or increases the frequency, rate or extent of the initiation of T cell receptor signaling." [GOC:mtg_signal] is_a: GO:0023010 ! regulation of initiation of T cell receptor signaling created_by: Jennifer I Deegan creation_date: 2009-12-02T11:08:34Z

[Term] id: GO:0023012 name: initiation of T cell receptor signaling by binding of a MHC complex to T cell receptor namespace: biological_process def: "The process whereby binding of an MHC complex to T cell receptor causes activation of T cell receptor signaling." [GOC:mtg_signal] is_a: GO:0023009 ! initiation of T cell receptor signaling relationship: has_part GO:0023023 ! MHC protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-02T11:10:16Z

[Term] id: GO:0023013 name: signal transmission via an intracellular cascade namespace: biological_process def: "The process whereby a signal is conveyed via an intracellular cascade." [GOC:mtg_signal] is_a: ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-12-02T11:28:45Z

[Term] id: GO:0023014 name: signal transmission via a phosphorylation event namespace: biological_process def: "The process whereby a signal is conveyed via a phosphorylation event." [GOC:mtg_signal] is_a: ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-12-02T11:32:55Z

[Term] id: GO:0023015 name: signal transmission via a cis-phosphorylation event namespace: biological_process def: "The process whereby a signal is conveyed via a cis-phosphorylation event." [GOC:mtg_signal] is_a: GO:0023014 ! signal transmission via a phosphorylation event created_by: Jennifer I Deegan creation_date: 2009-12-02T11:33:24Z

[Term] id: GO:0023016 name: signal transmission via a trans-phosphorylation event namespace: biological_process def: "The process whereby a signal is conveyed via a trans-phosphorylation event." [GOC:mtg_signal] is_a: GO:0023014 ! signal transmission via a phosphorylation event created_by: Jennifer I Deegan creation_date: 2009-12-02T11:33:35Z

[Term] id: GO:0023017 name: signal transmission via diffusible molecule namespace: biological_process alt_id: ID:0000005 def: "The process whereby a signal is conveyed via a diffusible molecule." [GOC:mtg_signal] synonym: "signaling via diffusible mediator" EXACT [] is_a: ID:0000027 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-12-02T11:35:34Z

[Term] id: GO:0023018 name: T cell activation of signal transmission via diffusible molecule namespace: biological_process def: "The process whereby signal transmission via a diffusible molecule is initiated by a T cell." [GOC:mtg_signal] is_a: GO:0023017 ! signal transmission via diffusible molecule created_by: Jennifer I Deegan creation_date: 2009-12-02T11:37:13Z

[Term] id: GO:0023019 name: regulation of gene expression as a consequence of signal transmission namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process whereby a signal is released and/or conveyed from one location to another." [GOC:mtg_signal] is_a: GO:0010468 ! regulation of gene expression is_a: ID:0000016 ! consequence of signal transmission created_by: Jennifer I Deegan creation_date: 2009-12-02T11:45:34Z

[Term] id: GO:0023020 name: regulation of gene expression as a consequence of T cell signal transmission namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process whereby a T cell signal is released and/or conveyed from one location to another." [GOC:mtg_signal] is_a: GO:0023019 ! regulation of gene expression as a consequence of signal transmission created_by: Jennifer I Deegan creation_date: 2009-12-02T11:46:15Z

[Term] id: GO:0023021 name: termination of signal transduction namespace: biological_process def: "The signaling process whereby signal transduction is brought to an end rather than being reversibly modulated." [GOC:mtg_signal] comment: Note that this term encompasses both the control point when the instruction is given for the process to cease and the actual cessation of the process. A process can persist for some time after that signal that induced the process is withdrawn. is_a: ID:0000012 ! signaling process created_by: Jennifer I Deegan creation_date: 2009-12-02T11:48:19Z

[Term] id: GO:0023022 name: termination of T cell signal transduction namespace: biological_process def: "The signaling process whereby T cell signal transduction is brought to an end rather than being reversibly modulated." [GOC:mtg_signal] is_a: GO:0023021 ! termination of signal transduction is_a: GO:0050860 ! negative regulation of T cell receptor signaling pathway created_by: Jennifer I Deegan creation_date: 2009-12-02T11:48:53Z

[Term] id: GO:0023023 name: MHC protein complex binding namespace: molecular_function is_a: GO:0003823 ! antigen binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:27:53Z

[Term] id: GO:0023024 name: MHC class I protein complex binding namespace: molecular_function is_a: GO:0023023 ! MHC protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:28:26Z

[Term] id: GO:0023025 name: MHC class Ib protein complex binding namespace: molecular_function is_a: GO:0023023 ! MHC protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:28:51Z

[Term] id: GO:0023026 name: MHC class II protein complex binding namespace: molecular_function is_a: GO:0023023 ! MHC protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:29:11Z

[Term] id: GO:0023027 name: MHC class I protein binding, via antigen binding groove namespace: molecular_function is_a: GO:0042288 ! MHC class I protein binding relationship: part_of GO:0023024 ! MHC class I protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:33:59Z

[Term] id: GO:0023028 name: MHC class I protein binding, via lateral surface namespace: molecular_function is_a: GO:0042288 ! MHC class I protein binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:34:16Z

[Term] id: GO:0023029 name: MHC class Ib protein binding namespace: molecular_function is_a: GO:0042287 ! MHC protein binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:35:37Z

[Term] id: GO:0023030 name: MHC class Ib protein binding, via antigen binding groove namespace: molecular_function is_a: GO:0023029 ! MHC class Ib protein binding relationship: part_of GO:0023025 ! MHC class Ib protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:36:03Z

[Term] id: GO:0023031 name: MHC class I protein binding, via lateral surface namespace: molecular_function is_a: GO:0023029 ! MHC class Ib protein binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:36:25Z

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