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. Diff taken from 1.516 (the branch point) to find list of terms. This was when signaling3.obo was created.

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." [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


8th January 2010

During a practise merge I have found that there are some duplicate ids in the signaling branch and live files. I have changed the ids in the signaling file as follows:

GO:0055125 changed to GO:0023032
GO:0055126 changed to GO:0023033
GO:0055127 changed to GO:0023034
GO:0055129 changed to GO:0023035

Still need to fix the ids that start ID:

11th January 2010

Fixed ids that started ID: as follows:

ID:0000000	GO:0023036 
ID:0000002	GO:0023037 
ID:0000003	GO:0023038 
ID:0000004	GO:0023039 
ID:0000006	GO:0023040 
ID:0000007	GO:0023041 
ID:0000008	GO:0023042 
ID:0000009	GO:0023043 
ID:0000010	GO:0023044 
ID:0000011	GO:0023045 
ID:0000012	GO:0023046 
ID:0000013	GO:0023047 
ID:0000014	GO:0023048 
ID:0000015	GO:0023049 
ID:0000016	GO:0023050 
ID:0000017	GO:0023051 
ID:0000018	GO:0023052 
ID:0000019	GO:0023053 
ID:0000020	GO:0023054 
ID:0000021	GO:0023055 
ID:0000022	GO:0023056 
ID:0000023	GO:0023057 
ID:0000025	GO:0023058 
ID:0000026	GO:0023059 
ID:0000027	GO:0023060 
ID:0000028	GO:0023061 
ID:0000029	GO:0023062 
ID:0000030	GO:0023063 
ID:0000031	GO:0023064 
ID:0000032	GO:0023065 
ID:0000033	GO:0023066 
ID:0000034	GO:0023067 
ID:0000035	GO:0023068 
ID:0000036	GO:0023069 
ID:0000037	GO:0023070

I just tried to merge the graph into the current live file, but OBOMerge is broken just now so I have not been successful. I have commented on the existing SF item on the subject.
https://sourceforge.net/tracker/index.php?func=detail&aid=2908106&group_id=36855&atid=418257

12th January 2010

Participants: Peter D'Eustachio, Sandra Orchard, Alex Diehl, Ruth Lovering, Jennifer Deegan.

We met and resolved the concerns raised at the GO Consortium meeting. Jennifer has checked the defs of the newly added terms. We decided to propose making the terms live at the end of January.

Action: Jennifer to send mail [DONE]

13th January 2010

Comment from Chris Mungall: "I'd be keen to see reactome xrefs added from the outset where possible - this would help 'concretize' the term and would help prevent future divergence of representation. Also perhaps the logical definitions too."

Peter D'Eustachio volunteers to do this:
If a "Reactome xref" is the identifier that we assign to the Reactome pathway instance that best matches a GO biological process instance (here, the new signaling instances), I should be able to do that. Coming up with a complete and definitive set may be hard, but I can certainly come up with a subset that will be useful at least as examples and can also come up with a subset where no xref exists because we don't have anything to say about that process yet (in case a negative control is useful).

Jennifer has asked if Peter would like to get together on the phone to consider how best to get him editing access to the file.