Annotation Conf. Call 2016-09-27: Difference between revisions
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#*BP Annotations | #*BP Annotations | ||
#:gpaB: GO:0032092 positive regulation of protein binding IDA, has_regulation_target GflB,rapA | #:gpaB: GO:0032092 positive regulation of protein binding IDA, has_regulation_target GflB,rapA | ||
#: gpaB: GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity IDA “request a PRO term for the active form?” | |||
#*MF annotations | #*MF annotations | ||
#: gflB: protein binding RapA happens_during GO:0001965 G-protein alpha-subunit binding | #: gflB: protein binding RapA happens_during GO:0001965 G-protein alpha-subunit binding | ||
#: gflB: small GTPase binding RapA happens_during activation of GTPase activity, has_direct_input gpaB | #: gflB: small GTPase binding RapA happens_during activation of GTPase activity, has_direct_input gpaB | ||
#: rapA: GO:0005515 protein binding GflB happens_during GO:0001965 G-protein alpha-subunit binding | #: rapA: GO:0005515 protein binding GflB happens_during GO:0001965 G-protein alpha-subunit binding | ||
#:rapA: GO:0005515 protein binding (gflB) happens_during activation of GTPase activity | #:rapA: GO:0005515 protein binding (gflB) happens_during activation of GTPase activity | ||
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=Minutes= | =Minutes= | ||
*On call: Bob, David H, Helen, George, Kimberly, Li, Midori, Olivia, Paola, Petra, Sabrina, Sage | *On call: Bob, David H, Helen, George, Kimberly, Li, Midori, Olivia, Paola, Paul T, Petra, Sabrina, Sage, Stan, Suzi | ||
==USC Meeting== | ==USC Meeting== | ||
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==Annotation Consistency Exercise== | ==Annotation Consistency Exercise== | ||
*Try to get wiki table and spreadsheet better aligned | *Try to get wiki table and spreadsheet better aligned | ||
**'''Action''': Send wiki compatible Excel table to all - DONE | |||
*Biggest question: How do we annotate that the binding bewteen GflB is dependent on the active (GTP-bound) form of the Galpha2 protein? | *Biggest question: How do we annotate that the binding bewteen GflB is dependent on the active (GTP-bound) form of the Galpha2 protein? | ||
**Possibly use PRO identifiers for capturing the active forms of entities like G proteins that are active when bound to a nucleotide | **Possibly use PRO identifiers for capturing the active forms of entities like G proteins that are active when bound to a nucleotide | ||
**How to capture the effect of Galpha2 on the activity of GflB? One possible solution: Galpha2 positive regulation of protein binding has_regulation_targets GflB and RapA | **How to capture the effect of Galpha2 on the activity of GflB? One possible solution: Galpha2 positive regulation of protein binding has_regulation_targets GflB and RapA | ||
**Use of happens_during does not capture the causal relation between the processes | **DH: Use of happens_during does not capture the causal relation between the processes | ||
** If a Pro term is available possible annotation: GflB GO:0017034 Rap guanyl-nucleotide exchange factor activity IDA has_input RapA, activated_by Pro / 'active Galpha' | |||
**'''Action''': Investigate if PRO (Prosite?? - not in P2GO and didn't get impression on first sight they add active form of a protein..) | |||
*Questions about annotation to regulation of myosin II assembly/disassembly | *Questions about annotation to regulation of myosin II assembly/disassembly | ||
**Do we need separate terms? | **Do we need separate terms? | ||
**Are these exactly opposite processes? If not, then keeping the terms separate would be best and we will need to add new terms. | **Are these exactly opposite processes? If not, then keeping the terms separate would be best and we will need to add new terms. | ||
**'''Action''': Create new term 'positive regulation of myosin II filament assembly' DONE by Termgenie, incl. 'negative regulation | |||
*Pan-ras antibody results | *Pan-ras antibody results | ||
**Older references support use of the specific Ras proteins based on use of the pan-ras antibody | **Older references support use of the specific Ras proteins based on use of the pan-ras antibody | ||
**Maybe a PRO term for Ras family proteins would be appropriate here, too | **Maybe a PRO term for Ras family proteins would be appropriate here, too | ||
**'''Action''' Keep specific ras extensions for this paper annotation - petra | |||
*Using SO identifiers to capture more granular information about sites of protein binding | *Using SO identifiers to capture more granular information about sites of protein binding | ||
**for example, occurs_at N-terminal region | **for example, occurs_at N-terminal region | ||
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**Is SO the appropriate ontology for capturing this information? | **Is SO the appropriate ontology for capturing this information? | ||
***SO has both amino acid and nucleotide sequence terms | ***SO has both amino acid and nucleotide sequence terms | ||
**We do an analogous thing for some DNA binding annotations but in these cases it's clear that the extension refers to the nucleotide | **Midori: We do an analogous thing for some DNA binding annotations but in these cases it's clear that the extension refers to the nucleotide | ||
**With protein binding annotations, it could be ambiguous as to which N-terminal region the annotation extension refers to | **With protein binding annotations, it could be ambiguous as to which N-terminal region the annotation extension refers to | ||
**If we could do nested expressions in annotation extensions, the meaning of this extension would be clearer | |||
**In a Noctua model, though, you could say that the N-terminal region is part_of the relevant entity | |||
**'''Action''': Delete this extension in linear annotation? | |||
*Other new term requests | |||
**Children of RasGTPase binding - need Rap GTPase binding | |||
**Guanylyl nucleotide exchange factor binding | |||
**Ontology editors are shying away from adding more of these binding terms as it is not sustainable | |||
**Preference would be given to allowing users to get this information by more sophisticated searches | |||
**There are currently so many binding terms, so even though we may not want more, then how do we justify not having a specific binding term when related binding terms are already there, e.g. Rap GTPase binding when Rac, Ras, Rho, etc. GTPase binding terms exist? | |||
**Discuss this at the November meeting - formal plan for modified form binding as well as specific protein terms | |||
***We need to make sure we don't lose information about who is binding whom | |||
***We want to support the search functionality that allows users to look for binding to specific types of proteins, but we don't necessarily want these terms in the ontology | |||
***Could we mine the information about the interacting partner's MF to inform the search | |||
***There are also annotation consistency issues wrt whether use of protein domain binding | |||
** '''Action''' Request no new binding term! | |||
*Will try to work on a LEGO model for this paper | |||
**Would be good to have a generic G protein signaling template | |||
[[Category: Annotation Working Group]] | [[Category: Annotation Working Group]] |
Latest revision as of 12:28, 29 September 2016
Bluejeans URL: https://bluejeans.com/993661940
Agenda
Meetings
Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016
- Please indicate on the Meeting Logistics Page if you plan to come.
- There is now a column for attending the GO dinner on Friday night. Please add your intention.
- There will be a one-day Noctua/LEGO training session for the Monday (November 7th) following the general consortium meeting. Please indicate on the logistics page if you are definitely staying for that so Paul T. can arrange for a meeting room.
GO Group Contacts
- Google spreadsheet sent out by ontology editors
- List of GO group members on github under people directory
- Does everyone have a github account?
- What is required for someone to be listed under People for the GO project?
- What is required to see everyone listed under People for the GO project?
Annotation Consistency Exercise
Abstract Chemotaxis, or directional movement toward extracellular chemical gradients, is an important property of cells that is mediated through G-protein-coupled receptors (GPCRs). Although many chemotaxis pathways downstream of Gβγ have been identified, few Gα effectors are known. Gα effectors are of particular importance because they allow the cell to distinguish signals downstream of distinct chemoattractant GPCRs. Here we identify GflB, a Gα2 binding partner that directly couples the Dictyostelium cyclic AMP GPCR to Rap1. GflB localizes to the leading edge and functions as a Gα-stimulated, Rap1-specific guanine nucleotide exchange factor required to balance Ras and Rap signaling. The kinetics of GflB translocation are fine-tuned by GSK-3 phosphorylation. Cells lacking GflB display impaired Rap1/Ras signaling and actin and myosin dynamics, resulting in defective chemotaxis. Our observations demonstrate that GflB is an essential upstream regulator of chemoattractant-mediated cell polarity and cytoskeletal reorganization functioning to directly link Gα activation to monomeric G-protein signalling.
Discussion Points
- What is the most appropriate annotation to describe how GflB binds to Rap1 (rapA), in the presence of ACTIVATED galpha2(gpaB)?
- BP Annotations
- gpaB: GO:0032092 positive regulation of protein binding IDA, has_regulation_target GflB,rapA
- gpaB: GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity IDA “request a PRO term for the active form?”
- MF annotations
- gflB: protein binding RapA happens_during GO:0001965 G-protein alpha-subunit binding
- gflB: small GTPase binding RapA happens_during activation of GTPase activity, has_direct_input gpaB
- rapA: GO:0005515 protein binding GflB happens_during GO:0001965 G-protein alpha-subunit binding
- rapA: GO:0005515 protein binding (gflB) happens_during activation of GTPase activity
- Do we need a new term ‘positive regulation of myosin II assembly’ Or is the current ‘regulation of myosin II assembly’ the positive regulation term as there is also ‘regulation of myosin II disassembly’, which is negative regulation of assembly?
- Ras protein specificity with Pan antibody assays. Use rasB, rasC, rasG in extension or not?
- Use of SO term to define where a protein binds another, but is extension occurs_at appropriate? Does it refer to first or second protein? Do we need a different relation, interacts_with?
- Annotation: gflB: GO:0001965 G-protein alpha-subunit binding IPI gpaB occurs_at SO:0100014 n_terminal_region
- Possible other new terms
- guanylyl-nucleotide exchange factor binding
- nucleitide exchange factor binding
- Rap GTPase binding as another child of 'Ras GTPase binding/', which has many other children
- LEGO
- Questions how to model this in Noctua, when is 'directly_activates' used and what is the correct ECO term for a nucleotide exchange assay (Fig. 2A? If not present, can it be added?
- LEGO model: http://noctua.berkeleybop.org/editor/graph/gomodel:57c82fad00000897#
Annotations
Gene/Marker Name | Qualifier | GO ID/term | Evidence Code | With/From | Annotation Extension | Comment | |
---|---|---|---|---|---|---|---|
Biological Process | |||||||
gflB | GO:0014066 regulation of phosphatidylinositol 3-kinase signaling | IMP | part_of GO:0050920 regulation of chemotaxis? will be clearer in LEGO | ||||
gflB | GO:0030837 negative regulation of actin polymerization | IMP | part_of GO:0050920 regulation of chemotaxis? presumably indirect, via effect on rapA activity; will be clearer in LEGO | ||||
gflB | GO:new (cf. GO:0043520) positive regulation of myosin II filament assembly | IMP | part_of GO:0050920 regulation of chemotaxis? presumably indirect, via effect on rapA activity; will be clearer in LEGO | ||||
gflB | GO:0046580 negative regulation of Ras protein signal transduction | IMP | part_of GO:0071320 cellular response to cAMP | 2e, 2f | |||
gflB | GO:0030010 establishment of cell polarity | IMP | part_of GO:0071320 cellular response to cAMP | s3b, 3a, s4a | |||
gflB | NTR: negative regulation of Akt/PKB singalling | IMP | 3b, 3c, s4b | ||||
gflB | NTR: negative regulation of actin polimerization | IMP | happens_during GO:0043327 chemotaxis to cAMP | 4a-c | |||
gflB | NTR: positive regulation of myosin II polimerization | IMP | happens_during GO:0043327 chemotaxis to cAMP | 4a-c | |||
gflB | GO:0043327 chemotaxis to cAMP | IMP | The observed developmental defects seem to be downstream of the cAMP signaling, so maybe in a LEGO diagram the process of chemotaxis to cAMP would have a positive causal relationship to the developmentl processes? Also, 'chemotaxis to cAMP' does not seem to have a relationship to 'response to cAMP' in the ontology. Should it? | ||||
gflB | GO:0071320 cellular response to cAMP | IMP | |||||
gflB | GO:0043547 positive regulation of GTPase activity | IMP | has_regulation_target Rap1 | ||||
gflB | GO:0034260 negative regulation of GTPase activity | IMP | RasB|RasC | I'm not sure if it's okay to put all of these specific Ras targets when a pan-Ras antibody was used. | |||
gflB | GO:0007264 small GTPase mediated signal transduction | IMP | |||||
gflB | GO:0030836 negative regulation of actin filament polymerization | IMP | I'm not sure about making this annotation; if I'm understanding the model correctly, the regulation would be indirect. | ||||
gflB | GO:new positive regulation of myosin II filament assembly | IMP | |||||
gflB | GO:0090630 activation of GTPase activity | IMP | has_regulation_target, happens_during, occurs_at rapA, response to cAMP, cell leading edge | as rap is in ras superfamily, this is the most specific term | |||
gflB | GO:0046580 negative regulation of Ras protein signal transduction | IMP | happens_during rasC, rasG, rasB , response to cAMP, cell leading edge | asexual reproduction | alternative term: negative regulation of GTPase activity | |||
gflB | GO:0061118 regulation of positive chemotaxis to cAMP | IMP | |||||
gflB | GO:0030837 negative regulation of actin filament polymerization | IMP | happens_during(GO:0051591) response to cAMP ,occurs_at(GO:0005886) plasma membrane | ||||
gflB | GO:0043520 regulation of myosin II filament assembly | IMP | happens_during(GO:0051591 response to cAMP ,occurs_at(GO:0005886) plasma membrane | ||||
gflB | GO:0030010 establishment of cell polarity | IMP | |||||
gflB | GO:0071901 negative regulation of protein serine/threonine kinase activity | IMP | has_input gflB | ||||
gflB | GO:0007264 small GTPase mediated signal transductions | IMP | has_regulation_target pkbA, pkgA | ||||
gflB | GO:0030837 negative regulation of actin filament polymerisation | IMP | |||||
gflB | GO:0043520 regulation of myosin II filament assembly | IMP | |||||
gflB | GO:0006935 chemotaxis | IMP | |||||
gflB | GO:0046579 positive regulation of Ras protein signal transduction | IMP | |||||
gflB | GO:0061122 positive regulation of positive chemotaxis to cAMP | IMP | pg 460 right column | ||||
gflB | GO:0032487 regulation of Rap protein signal transduction | IMP | has input: rapA GO:0071320|UniProt: P18613 | may need to request "positive regulation of Rap signal transduction; pg 461 right column | |||
gflB | GO:0046580 negative regulation of Ras protein signal transduction | IMP | happens during: cellular response to cAMP GO:0071320 | no input here as it could be RasG, RasB and or RasC; pg 461 right column | |||
gflB | GO:0030838 positive regulation of actin filament polymerisation | IMP | occurs at: cell leading GO:0071320|GO:0031252 | pg 462 right column | |||
gflB | GO:0043520 regulation of myosin II filament assembly | IMP | occurs at: cell leading GO:0071320|GO:0031252 | may need to request "positive regulation of myosin II filament assembly; pg 462 right column | |||
gflB | GO:0043327 chemotaxis to cAMP | IMP | |||||
gflB | GO:0046580 negative regulation of Ras protein signal transduction | IMP | regulates_o_has_participant RasG | ||||
gflB | GO:0046579 positive regulation of Ras protein signal transduction | IMP | regulates_o_has_participant Rap1 | ||||
gflB | GO:0030837 negative regulation of actin filament polymerisation | IMP | |||||
gflB | GO:0043520 regulation of myosin II filament assembly | IMP | ask for positive regulation term | ||||
gflB | GO:0061339 establishment or maintenance of monopolar cell polarity | ||||||
gflB | GO:0060326 cell chemotaxis | IMP | |||||
gflB | GO:0046580 negative regulation of Ras protein signal transduction | happens_during GO:0060326 cell chemotaxis | |||||
gflB | GO:0032487 regulation of Rap protein signal transduction | IMP | happens_during GO:0060326 cell chemotaxis | ||||
gflB | GO:0032487 regulation of Rap protein signal transduction | IMP | has_regulation_target UniProtKB:P18613 | RAP1 is target | |||
gpaB | GO:0043327 chemotaxis to cAMP | IMP | Table 1, Figure 1, Movies S1-S3. | ||||
gpaB | GO:0048468 cell development | IMP | S1e | ||||
gpaB | GO:0032092 positive regulation of protein binding | IDA | has_regulation_target GflB,rapA | I'm not sure the exact meaning of this annotation is clear, i.e. that gpaB is regulating the binding of GflB to rapA. | |||
gpaB | GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity | IDA | has_regulation_target, occurs_at gflB, GO:1904269 cell leading edge cell cortex | ||||
gpaB | GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity | IDA | has regul;ation target: gflB UniProt: Q54L90 | pg 461 left column | |||
gpaB | GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity | IDA | request a PRO term for the active form? | ||||
gskA | GO:0006468 protein phosphorylation | IDA | has_input AND negatively_regulates gflB (DDB_G0286773) AND GO:0072697 protein localization to cell cortex | 5d, 5e | |||
gskA | GO:1904777 negative regulation of protein localization to cell cortex | IMP | has_regulation_target gflB (DDB_G0286773) | 5e | |||
gskA | GO:0018105 peptidyl serine phosphorylation | IMP | |||||
gskA | GO:0018107 peptidyl threonine phosphorylation | IMP | |||||
gskA | GO:1904776 regulation of protein localization to cell cortex | IMP | has_regulation_target GflB | ||||
gskA | GO:0006468 protein phosphorylation | IDA | has_input gflB | ||||
gskA | GO:1904776 regulation of protein localization to cell cortex | IMP | has_regulation_target, occurs_at gflB, leading edge | ||||
gskA | GO:0018105 peptidyl-serine phosphorylation | IMP | has input: gflB UniProt: Q54L90 | pg 464 right column | |||
gskA | GO:0018107 peptidyl-threonine phosphorylation | IMP | has input: gflB UniProt: Q54L90 | pg 464 right column | |||
gskA | GO:1904777 negative regulation of protein localization to cell cortex | IMP | happens during: cellular response to cAMP UniProt: Q54L90|GO:0071320 | pg 464 right column | |||
gskA | GO:0006468 protein phosphorylation | IMP | has_input GflB | ||||
gskA | GO:1902463 protein localization to cell leading edge | transports or maintains localization of GflB | |||||
rapA | GO:0071320 cellular response to cAMP | IEP | |||||
rasB | GO:0071320 cellular response to cAMP | IEP | See above comment on pan-Ras antibody. | ||||
rasC | GO:0071320 cellular response to cAMP | IEP | See above comment on pan-Ras antibody. | ||||
rasG | GO:0071320 cellular response to cAMP | IEP | See above comment on pan-Ras antibody. | ||||
Molecular Function | |||||||
gflB | GO:0017034 Rap guanyl-nucleotide exchange factor activity | IDA | has_regulation_target Rap1 | ||||
gflB | GO:0005515 protein binding | IDA | Ga2 | ||||
gflB | GO:0005515 protein binding | IPI | Rap1 | how to capture "requires presence of active Ga2" in conventional annotation? (I'm not even sure how to do it in LEGO) | |||
gflB | NOT | NTR: Rho GTPase activator activity | IDA | S2b-d | |||
gflB | GO:0005088 Ras guanyl-nucleotide exchange factor activity | IMP | 2a | ||||
gflB | GO:0001965 G-protein alpha-subunit binding | IPI | gpaB (DDB_G0276267) | 1b | |||
gflB | GO:0005515 protein binding | IPI | rapA (DDB_G0291237) | happens_during GO:0001965 G-protein alpha-subunit binding | s2e + 2b | ||
gflB | NTR: activation of Rap1 GTPase activity | IMP | part_of GO:0071320 cellular response to cAMP | ||||
gflB | GO:0001965 G-protein alpha-subunit binding | IPI | gpaB | occurs_at SO:0100014 n_terminal_region | SO term is defining where gflB binds to gpaB - need new relation? | ||
gflB | GO:0031267 small GTPase binding | IPI | RapA | happens_during, has_direct_input activation of GTPase activity, gpaB | maybe Rap GTPase binding should be added as child, all others are there | ||
gflB | GO:0017034 Rap guanyl-nucleotide exchange factor activity | IDA | has_input, happens_during, occurs_at rapA,activation of GTPase activity, cell cortex | ||||
gflB | GO:0005543 phospholipid binding | IDA | occurs_at SO:0100014 n_terminal_region | Fig.5SA | |||
gflB | GO:0001965 G-protein alpha-subunit binding | IPI | gpaB | activated by GppNHp (CHEBI:78408) | or should this be GTP (CHEBI:15996); pg 460 left column | ||
gflB | GO:0017034 Rap guanyl-nucleotide exchange factor activity | IDA | has regulation target: rapA UniProt: P18613 | pg 461 left column | |||
GflB | GO:0005515 protein binding | IPI | GpaB | ||||
GflB | GO:0005085 guanyl-nucleotide exchange factor activity | IMP | |||||
GflB | GO:0005085 guanyl-nucleotide exchange factor activity | IDA | has_input Rap1 | ||||
GflB | GO:0005515 protein binding | IPI | Rap1 | has_participant GpaB | depends on Ga2 being bound to GPPnHp | ||
GflB | GO:0005515 protein binding | IPI | GpaB | ||||
GflB | GO:0005515 protein binding | IPI | RACB, RACL | ||||
GflB | GO:0005085 guanyl-nucleotide exchange factor activity | IDA | has_direct_input UniProtKB:P18613 | RAP1 is target | |||
gpaB | GO:0005515 protein binding | IPI | gflB (DDB_G0286773) | 1b | |||
gpaB | NTR: Ras guanyl-nucleotide exchange factor binding | IC | GO:0005515 protein binding | 1 | |||
gpaB | GO:0032092 positive regulation of protein binding | IDA | has_regulation_target AND has_regulation_target gflB (DDB_G0286773) AND rapA (DDB_G0291237 | 2b | |||
gpaB | GO:0005515 protein binding | IPI | GflB | Possibly a new term for guanylyl-nucleotide exchange factor binding? Also, see above. | |||
gpaB | GO:0005515 protein binding | IPI | gflB | part_of GO:0007186 G-protein coupled receptor signaling pathway | maybe new term 'nucleitide exchange factor binding? Cannot easily annotate that only activated (GTP bound) gpbA binds to gflB | ||
GpaB | GO:0005515 protein binding | IPI | GflB | ||||
GskA | GO:0004674 protein serine/threonine kinase activity | IDA | has_direct_input GflB | ||||
GskA | GO:0004674 protein serine/threonine kinase activity | IMP | happens_during, part_of, has_regulation_target GO:0071320, GO:1905097, GflB | full extension: happens_during GO:0071320, part_of GO:1905097, has_regulation_target GflB (GO:0071320 = cellular response to cAMP; GO:1905097 = regulation of guanyl-nucleotide exchange factor activity) | |||
gskA | GO:0004674 protein serine/threonine kinase activity | IDA | has_input gflB (DDB_G0286773) | 5d | |||
GskA | GO:0004674 protein serine/threonine kinase activity | ISS | human GSK3b | has input GflB | |||
GskA | GO:0004674 protein serine/threonine kinase activity | IDA | has_direct_input UniProtKB:Q54L90 | ||||
RACB | GO:0005515 protein binding | IPI | GflB | Fig. S1 | |||
RACL | GO:0005515 protein binding | IPI | GflB | Fig. S1 | |||
rapA | GO:0005515 protein binding | IPI | gflB (DDB_G0286773) | happens_during GO:0001965 G-protein alpha-subunit binding | s2e + 2b | ||
rapA | GO:0005515 protein binding | IPI | GflB | ||||
rapA | GO:0005515 protein binding | IPI | GflB | happens_during activation of GTPase activity | new term 'nucleitide exchange factor binding? | ||
Cellular Component | |||||||
gflB | GO:0005737 cytoplasm | IDA | unstimulated cells | ||||
gflB | GO:1904269 cell leading edge cell cortex | IDA | unstimulated cells | ||||
gflB | GO:0005938 cell cortex | IDA | exists_during GO:0071320 | GO:0071320 = cellular response to cAMP; not sure how to capture cytoskeleton dependency, in conventional annotation extensions or LEGO; does the experiment with GflBP1 and LatA show plasma membrane GO:0005886? | |||
gflB | GO:0005737 cytoplasm | IDA | 5a | ||||
gflB | GO:0005737 cytoplasm | IDA | exists_during asexual reproduction | ||||
gflB | GO:0005938 cell cortex | IDA | exists_during response to cAMP | ||||
gflB | GO:0031252 cell leading edge | IDA | exists_during chemotaxis to cAMP | ||||
gflB | GO:0005886 plasma membrane | IDA | exists_during chemotaxis to cAMP | annotated 'plasma membrane' because of latA + domain expression experiments, also Supp Fig. 5A shows Phospholipid binding (see MF) | |||
GflB | GO:0005938 cell cortex | IDA | |||||
GflB | GO:0031252 cell leading edge | IDA | exists_during chemotaxis (GO:0006935) | ||||
gflB | GO:0005737 cytoplasm | IDA | pg 462 right column | ||||
gflB | GO:0031252 cell leading edge | IDA | exists during: cell chemotaxis GO:0060326 | gradient treatment to induce chemotaxis; pg 462 right column | |||
gflB | GO:0005938 cell cortex | IDA | happens during: cellular response to cAMP GO:0071320 | uniform or global treatment with cAMP; pg 462 right column | |||
gflB | GO:0031256 leading edge membrane | IDA | |||||
gflB | GO:0031252 cell leading edge | IDA | |||||
gflB | GO:1904269 cell leading edge cell cortex | IDA | localization_dependent_on ?Galpha2 | requires binding of active Galpha | |||
Raf1 | GO:1904269 cell leading edge cell cortex | IDA | |||||
Ral | GO:1904269 cell leading edge cell cortex | IDA | |||||
Rap1 | GO:0009279 cell outer membrane | IDA | |||||
Rap1 | GO:0005886 plasma membrane | IDA | |||||
rapA | GO:0005886 plasma membrane | IDA | 3a | ||||
rapA | GO:0005886 plasma membrane | IDA | |||||
rasG | GO:0005886 plasma membrane | IDA | 3a | ||||
RasG | GO:0005886 plasma membrane | IDA | |||||
RasG | GO:0009279 cell outer membrane | IDA | |||||
RasG | GO:0005886 plasma membrane | IDA |
Minutes
- On call: Bob, David H, Helen, George, Kimberly, Li, Midori, Olivia, Paola, Paul T, Petra, Sabrina, Sage, Stan, Suzi
USC Meeting
- Please double-check the table and fill in for meeting, dinner, and the Noctua workshop.
- Let Seth know if you need access to the Noctua tool
- Also check Quick Start Guide linked from Noctua homepage for instructions on how to login
Contact Information
- GO editors sent out a Google spreadsheet for contact information for each group
- Most groups on this call have filled this sheet out
- Paola will try to find contacts for the other groups on the spreadsheet who no longer regularly attend the annotation calls
- Please get a github account if you'd like to contribute to any of the GO repositories, e.g. ontology requests
- Users will need to be invited to a repository in order to have their name on the autocomplete list for a repository
- PomBase is trying to set up a generic username for them to allow relevant notices sent to their helpdesk
Annotation Consistency Exercise
- Try to get wiki table and spreadsheet better aligned
- Action: Send wiki compatible Excel table to all - DONE
- Biggest question: How do we annotate that the binding bewteen GflB is dependent on the active (GTP-bound) form of the Galpha2 protein?
- Possibly use PRO identifiers for capturing the active forms of entities like G proteins that are active when bound to a nucleotide
- How to capture the effect of Galpha2 on the activity of GflB? One possible solution: Galpha2 positive regulation of protein binding has_regulation_targets GflB and RapA
- DH: Use of happens_during does not capture the causal relation between the processes
- If a Pro term is available possible annotation: GflB GO:0017034 Rap guanyl-nucleotide exchange factor activity IDA has_input RapA, activated_by Pro / 'active Galpha'
- Action: Investigate if PRO (Prosite?? - not in P2GO and didn't get impression on first sight they add active form of a protein..)
- Questions about annotation to regulation of myosin II assembly/disassembly
- Do we need separate terms?
- Are these exactly opposite processes? If not, then keeping the terms separate would be best and we will need to add new terms.
- Action: Create new term 'positive regulation of myosin II filament assembly' DONE by Termgenie, incl. 'negative regulation
- Pan-ras antibody results
- Older references support use of the specific Ras proteins based on use of the pan-ras antibody
- Maybe a PRO term for Ras family proteins would be appropriate here, too
- Action Keep specific ras extensions for this paper annotation - petra
- Using SO identifiers to capture more granular information about sites of protein binding
- for example, occurs_at N-terminal region
- Groups may differ on this point - some curators might want to add this, others would not go into this much detail
- Is SO the appropriate ontology for capturing this information?
- SO has both amino acid and nucleotide sequence terms
- Midori: We do an analogous thing for some DNA binding annotations but in these cases it's clear that the extension refers to the nucleotide
- With protein binding annotations, it could be ambiguous as to which N-terminal region the annotation extension refers to
- If we could do nested expressions in annotation extensions, the meaning of this extension would be clearer
- In a Noctua model, though, you could say that the N-terminal region is part_of the relevant entity
- Action: Delete this extension in linear annotation?
- Other new term requests
- Children of RasGTPase binding - need Rap GTPase binding
- Guanylyl nucleotide exchange factor binding
- Ontology editors are shying away from adding more of these binding terms as it is not sustainable
- Preference would be given to allowing users to get this information by more sophisticated searches
- There are currently so many binding terms, so even though we may not want more, then how do we justify not having a specific binding term when related binding terms are already there, e.g. Rap GTPase binding when Rac, Ras, Rho, etc. GTPase binding terms exist?
- Discuss this at the November meeting - formal plan for modified form binding as well as specific protein terms
- We need to make sure we don't lose information about who is binding whom
- We want to support the search functionality that allows users to look for binding to specific types of proteins, but we don't necessarily want these terms in the ontology
- Could we mine the information about the interacting partner's MF to inform the search
- There are also annotation consistency issues wrt whether use of protein domain binding
- Action Request no new binding term!
- Will try to work on a LEGO model for this paper
- Would be good to have a generic G protein signaling template