Annotation Conf. Call 2016-10-25: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
 
(34 intermediate revisions by 3 users not shown)
Line 8: Line 8:
*Register for meeting and dinner, just dinner, just meeting.
*Register for meeting and dinner, just dinner, just meeting.
*No registration fee for the Noctua workshop.
*No registration fee for the Noctua workshop.
*[http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda Draft Agenda] - please review


==Discussion of Outstanding github Tickets==
==Discussion of Outstanding github Tickets==
*[https://github.com/geneontology/go-ontology/issues/12543 NTR: maintenance of differentiated cell state]
*[https://github.com/geneontology/go-ontology/issues/12543 NTR: maintenance of differentiated cell state]
*Paper: [https://www.ncbi.nlm.nih.gov/pubmed/24804980 miR-1, miR-10b, miR-155, and miR-191 are novel regulators of BDNF.]
*[http://noctua.berkeleybop.org/editor/graph/gomodel:580685bd00000264 accompanying LEGO model]


==Annotation Consistency Exercise==
==Annotation Consistency Exercise==
Line 19: Line 22:
CONCLUSION:It is concluded that the intestine takes up iron through a sequential transfer involving interaction of luminal transferrin, transferrin-transferrin receptor and ferritin.<br />
CONCLUSION:It is concluded that the intestine takes up iron through a sequential transfer involving interaction of luminal transferrin, transferrin-transferrin receptor and ferritin.<br />
<br />
<br />
 
'''Discussion Points'''
<br />
# What can be done with ferritin annotations, since a specific subunit was non identified in the paper? 
# Should colocalization (IEP) data be used for biological process annotations?
# If an iron transport annotation is made, does an iron homeostasis annotation impart any additional information?
# Is "intestinal absorption" too broad?  Should an intestinal iron absorption term be requested?
'''Accompanying LEGO Model'''
*[http://noctua.berkeleybop.org/editor/graph/gomodel:580685bd00000086 iron absorption in the intestine]
'''Annotations'''
'''Annotations'''
{| class="wikitable" border="1"
{| class="wikitable" border="1"
|-
|-
! Gene/Marker Name
! Gene Symbol, Gene Name
! Qualifier
! GO term/ID
! GO ID/term
! Evidence Code
! Evidence Code
! With/From
! Annotation Source
! Annotation Extension  
! Annotation Extension  
! Comment
! Comment
|-
|-
|''Biological Process''
!''Biological Process''
|-
| gene
|
| GOID term
| evidence code
|
|
| comment
|-
|-
| gflB
| ferritin
| iron ion transport GO:0006826
| IDA
| FB, Tair
|
|
| GO:0030837 negative regulation of actin polymerization
| Which ferritin subunit?
| IMP
|-  
|
| Tf, transferrin
|
| iron ion transport GO:0006826
| 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
|
| has_regulation_target RasG|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
|
| has_regulation_target, happens_during, occurs_at | 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
|
| happens during: cellular response to cAMP| 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
|
| happens during: cellular response to cAMP| occurs at: cell leading GO:0071320|GO:0031252
| pg 462 right column
|-
| gflB
|
| GO:0043520 regulation of myosin II filament assembly
| IMP
|
| happens during: cellular response to cAMP| 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
| IDA
| FB, Tair
|
|
| has_regulation_target GflB,rapA
| transport is inferred from radioactive Fe sequential colocalizing with location of each of the proteins in different parts of the duodenum
| 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
| Tfrc, transferrin receptor
|
| iron ion transport GO:0006826
| GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity
| IDA
| IDA
| FB, Tair
|
|
| has_regulation_target, occurs_at gflB, GO:1904269 cell leading edge cell cortex
| Tfrc or Tfr2?
|
|-
|-
| gpaB
| Tf, transferrin
|
| ferric iron transport GO:0015682
| GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity
| IDA
| IDA
| RGD
|
|
| has regul;ation target: gflB UniProt: Q54L90
|  
|pg 461 left column
|-
|-
| gpaB
| ferritin
|
| ferric ion import GO:0033216
| GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity
| IDA
| IDA
|
| SGD
|
|occurs_in UBERON:0000320 duodenal mucosa
| request a PRO term for the active form?
| Which ferritin?
 
|-  
|-
| Tf, transferrin
| gskA
| ferric ion import GO:0033216
|
| GO:0006468 protein phosphorylation
| IDA
| IDA
|
| SGD
| has_input AND negatively_regulates gflB (DDB_G0286773) AND GO:0072697 protein localization to cell cortex
|occurs_in UBERON:0000320 duodenal mucosa
| 5d, 5e
|  
|-
|-
| gskA
| Tf, transferrin
| GO:0098706 -ferric iron import across plasma membrane
| IEP
| WB
|
|
| GO:1904777 negative regulation of protein localization to cell cortex
|  
| IMP
|
| has_regulation_target gflB (DDB_G0286773)
| 5e
|-
|-
| gskA
| Tfrc, transferrin receptor
|
| GO:0098706 -ferric iron import across plasma membrane
| GO:0018105 peptidyl serine phosphorylation
| IEP
| IMP
| WB
|
|
|
|
|
|-
|-
| gskA
| ferritin
| iron ion homeostasis GO:0055072
| IDA
| FB
|
|
| GO:0018107 peptidyl threonine phosphorylation
| Which ferritin subunit?
| IMP
|-  
|
| Tf, transferrin
|
| iron ion homeostasis GO:0055072
|
| IDA
|-
| FB
| gskA
|
| GO:1904776 regulation of protein localization to cell cortex
| IMP
|
| has_regulation_target GflB
|
|
| transport is inferred from radioactive Fe sequential colocalizing with location of each of the proteins in different parts of the duodenum
|-
|-
| gskA
| Tfrc, transferrin receptor
|
| iron ion homeostasis GO:0055072
| GO:0006468 protein phosphorylation
| IDA
| IDA
| FB
|
|
|has_input gflB
|  
|
|-
|-
| gskA
| ferritin, Fth1, Ftl1
|
| GO:0060586 - multicellular organismal iron ion homeostasis
| GO:1904776 regulation of protein localization to cell cortex
| IEP
| IMP
| WB
|
| occurs_in(UBERON:0000320) duodenal mucosa|occurs_in(UBERON:0016512) lumen of duodenum
| has_regulation_target, occurs_at  gflB, leading edge
|  
|
|-  
|-
| Tf, transferrin
| gskA
| GO:0060586 - multicellular organismal iron ion homeostasis
|
| IEP
| GO:0018105 peptidyl-serine phosphorylation
| WB
| IMP
| occurs_in(UBERON:0016512)lumen of duodenum
|
| 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
|  
|  
| has regulation target: gflB|happens during: cellular response to cAMP UniProt: Q54L90|GO:0071320
|  pg 464 right column
|-
|-
| gskA
| Tfrc, transferrin receptor
|
| GO:0060586 - multicellular organismal iron ion homeostasis
| GO:0006468 protein phosphorylation
| IEP
| IMP
| WB
|
| occurs_in(UBERON:0002114) duodenum
| has_input GflB
|
|
|-
| Tf, transferrin
| GO:0050892 - intestinal absorption
| IEP
| WB
| has_input(ChEBI:29034)
| Maybe request "intestinal iron ion absorption".
|-
|-
| gskA
| Tfrc, transferrin receptor
| GO:0050892 - intestinal absorption
| IEP
| WB
| has_input(ChEBI:29034)
|
|
| GO:1902463 protein localization to cell leading edge
|-  
|
| Tf, transferrin
|
| response to iron ion GO:0010039
| transports or maintains localization of GflB
|
|-
| rapA
|
| GO:0071320 cellular response to cAMP
| IEP
| IEP
|
| RGD
|
|  
|
| movement between compartments dependent on iron level in diet
|-
|-
| rasB
| Tfrc, transferrin receptor
|
| response to iron ion GO:0010039
| GO:0071320 cellular response to cAMP
| IEP
| IEP
| RGD
|
|
|
|
| See above comment on pan-Ras antibody.
|-  
|-
| human ferritin, FTH1 (UniProtKB:P02794), FTL (UniProtKB:P02792)
| rasC
| GO:0060586 - multicellular organismal iron ion homeostasis
|
| GO:0071320 cellular response to cAMP
| IEP
| IEP
|
| WB
|
| occurs_in(UBERON:0002114) duodenum
| See above comment on pan-Ras antibody.
|  
|-
|-  
| rasG
| human TF (UniProtKB:P02787)
|
| GO:0060586 - multicellular organismal iron ion homeostasis
| GO:0071320 cellular response to cAMP
| IEP
| IEP
|
| WB
|
| occurs_in(UBERON:0002114) duodenum
| See above comment on pan-Ras antibody.
|  
|-
|-
| ''Molecular Function''
|-  
|-  
| gflB
| human TFRC (UniProtKB:P02786)
|
| GO:0060586 - multicellular organismal iron ion homeostasis
| GO:0017034 Rap guanyl-nucleotide exchange factor activity
| IEP
| IDA
| WB
|
| occurs_in(UBERON:0002114) duodenum
| 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''
!''Cellular Component''
|-  
|-  
|-
| Tf, transferrin
| gflB
| cell tip GO:0051286
|
| GO:0005737 cytoplasm
| IDA
| IDA
| RGD
|  
|  
|
| Figure 5 - ID, 15 min; text description
| unstimulated cells
|-
|-
| gflB
| Tfrc, transferrin receptor
|
| cell surface GO:0009986
| GO:1904269 cell leading edge cell cortex
| IDA
| IDA
| RGD
|
|
|
| Figure 5; text description
| unstimulated cells
|-  
|-
| Tfrc, transferrin receptor
| gflB
| GO:0031528 - microvillus membrane
|
| GO:0005938 cell cortex
| IDA
| IDA
|
| WB
| 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
| Tf, transferrin, Fth1, Ftl1, ferritin
|
| GO:0005615 - extracellular space
| GO:0005737 cytoplasm
| IDA
| IDA
|
| WB
|
|  
| 5a
|  
|-
|-
| gflB
!''Molecular Function''
|
| GO:0005737 cytoplasm
| IDA
|
| exists_during asexual reproduction
|
|-
|-
| gflB
| Fth1, Ftl1, ferritin
|
| iron ion binding, GO:0005506
| GO:0005938 cell cortex
| IDA
| IDA
|
| FB, Tair, WB
| exists_during response to cAMP
| occurs_in UBERON:0000320 duodenal mucosa
|
| Which ferritin subunit?
|-
|-
| gflB
| Tf, transferrin
|
| iron ion binding, GO:0005506
| GO:0031252 cell leading edge
| IDA
| IDA
|
| FB, Tair, WB
| exists_during chemotaxis to cAMP
| occurs_in UBERON:0000320 duodenal mucosa
|
|
|-
|-
| gflB
| Tf, transferrin
|
| ferric iron binding GO:0008199
| GO:0005886 plasma membrane
| IDA
| IDA
| RGD, SGD
|
|
|
| exists_during chemotaxis to cAMP
|  annotated 'plasma membrane' because of latA + domain expression experiments, also Supp Fig. 5A shows Phospholipid binding (see MF)
|-
|-
| GflB
| ferritin
|
| ferric iron binding GO:0008199
| GO:0005938 cell cortex
| IDA
| IDA
|
| SGD
|
|  
|
| Which ferritin?
|-
|-
| GflB
| Tfrc, transferrin receptor
|
| GO:0004998 - transferrin receptor activity
| GO:0031252 cell leading edge
| IEP
| IDA
| WB
|
| occurs_in(UBERON:0008346) duodenal epithelium
| exists_during chemotaxis (GO:0006935)
| IEP for MF annotation???
|
|-
| 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=
=Minutes=
*On call:
*On call: Alice, Barbara, Edith, Giulia, Helen, Kimberly, Li, Midori, Olivia, Paola, Paul T., Penelope, Petra, Sabrina, Sage, Stacia, Stan, Tanya, Val
 
==Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016==
*Please register if you haven't already
*Please check the meeting agenda to see what topics will be discussed
**If you are interested in raising a topic for discussion, please add it along with your name and the amount of time you think will be needed
 
==Annotation Consistency Exercise==
*Issues we discussed:
**Determining what annotations could be made to ferritin
***Authors used an antibody, but didn't say exactly what the antibody recognized and there are many different potential subunits to the rat ferritin complex (light and heavy chains)
**Differences in evidence code usage
***Most curators used IDA for the transport annotations, but there was also IEP
***There was some discussion about use of IC to support annotations, as there didn't seem to be a single experiment that showed both iron binding and transport
**Support for iron homeostasis annotations?
***We discussed whether an iron homeostasis annotation added much if the proteins were already annotated to irton transport
***Did the experiments simply show support for nutrient uptake or was there also support for homeostasis?
**Annotations to intestinal absorption
***Seems a broad, high level term to use, but could be made more specific with annotation extensions, e.g. has_input(ferric ion), or by requesting a new, more granular term like intestinal iron absoption.
***For terms like intestinal iron absorption, the potential list of terms could get very long - is this necessary?  Would an alternative term such as intestinal metal ion absorption be a reasonable alternative?
**Additional papers with knock-down experiments might help to better support the Biological Process annotations
**Cellular component annotations
***What evidence is sufficient to annotate to cell surface vs a membrane term?  Note that this issue has been raised before and will be discussed at the GOC meeting next month.
**Molecular function annotations
***What evidence would support the transferrin receptor activity annotation?  Maybe IC, but not IEP.
*Review of Noctua model:
**Ferritin is represented in this model by the generic GO complex, so no specific annotations to a rat complex, or particular subunits, would be made
**The model represents the relation between transferrin and the transferrin receptor as 'directly provides input for'
***David was not certain that this was the best relation to use, but wanted to capture the idea that there was some sort of causal relation between the transferrin and the transferrin receptor that led to uptake into the epithelium
**Note that it would be fine to use evidence from more than one paper to support a given LEGO model
 
==Discussion of Outstanding github Tickets==
*We discussed two issues surrounding an ontology request for a new term [https://github.com/geneontology/go-ontology/issues/12543 maintenance of differentiated cell state]
*The first involved what is generally meant by 'maintenance of differentiation'
**Would this term refer to a developmental process or program that specifically controls de-differentiation after a cell has fully differentiated and a change in its environment results in reversion to an undifferentiated state? Or, does this refer to a process that is simply part of differentiation?
**What experiments would adequately demonstrate a distinction between these two?
*The second involved what is meant by 'positive regulation of a process' and whether that includes the concept of maintenance of that process
**The website guidelines on regulation specifically include 'maintenance', along with 'activation' and 'upregulation', of a process as positive regulation of that process - see http://geneontology.org/page/regulation
**However, the existing term definitions for 'positive regulation of biological process' do not specifically state that this includes maintenance; they only refer to 'Any process that activates or increases the frequency, rate or extent of a biological process.' - see http://amigo.geneontology.org/amigo/term/GO:0048518
**Should the definition of 'positive regulation of biological process' term (and its children) explicitly refer to maintenance as well as activation and induction?
**Do we have examples of process maintenance that is considered regulation of that process? 
**Requested that this issue be added to an ontology editors call




[[Category: Annotation Working Group]]
[[Category: Annotation Working Group]]

Latest revision as of 11:33, 26 October 2016

Bluejeans URL: https://bluejeans.com/993661940

Agenda

Meetings

Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016

  • Link to a registration form is now available for the USC Meeting on the Meeting Logistics Page.
  • Register for meeting and dinner, just dinner, just meeting.
  • No registration fee for the Noctua workshop.
  • Draft Agenda - please review

Discussion of Outstanding github Tickets

Annotation Consistency Exercise

Abstract AIM:To elucidate the sequential transfer of iron amongst ferritin, transferrin and transferrin receptor under various iron status conditions. METHODS:Incorporation of 59Fe into mucosal and luminal proteins was carried out in control WKY rats. The sequential transfer of iron amongst ferritin, transferrin and transferrin receptor was carried out in iron deficient, control and iron overloaded rats. The duodenal proteins were subjected to immunoprecipitation and quantitation by specific ELISA and in situ localization by microautoradiography and immunohistochemistry in tandem duodenal sections. Human duodenal biopsy (n = 36) collected from subjects with differing iron status were also stained for these proteins. RESULTS:Ferritin was identified as the major protein that incorporated iron in a time-dependent manner in the duodenal mucosa. The concentration of mucosal ferritin was significantly higher in the iron excess group compared to control, iron deficient groups (731.5 +/- 191.96 vs 308.3 +/- 123.36, 731.5 +/- 191.96 vs 256.0 +/- 1.19, P < 0.005), while that of luminal transferrin which was significantly higher than the mucosal did not differ among the groups (10.9 +/- 7.6 vs 0.87 +/- 0.79, 11.1 +/- 10.3 vs 0.80 +/- 1.20, 6.8 +/- 4.7 vs 0.61 +/- 0.63, P < 0.001). In situ grading of proteins and iron, and their superimposition, suggested the occurrence of a sequential transfer of iron. This was demonstrated to occur through the initial binding of iron to luminal transferrin then to absorptive cell surface transferrin receptors. The staining intensity of these proteins varied according to the iron nutrition in humans, with intense staining of transferrin receptor observed in iron deficient subjects. CONCLUSION:It is concluded that the intestine takes up iron through a sequential transfer involving interaction of luminal transferrin, transferrin-transferrin receptor and ferritin.

Discussion Points

  1. What can be done with ferritin annotations, since a specific subunit was non identified in the paper?
  2. Should colocalization (IEP) data be used for biological process annotations?
  3. If an iron transport annotation is made, does an iron homeostasis annotation impart any additional information?
  4. Is "intestinal absorption" too broad? Should an intestinal iron absorption term be requested?

Accompanying LEGO Model

Annotations

Gene Symbol, Gene Name GO term/ID Evidence Code Annotation Source Annotation Extension Comment
Biological Process
ferritin iron ion transport GO:0006826 IDA FB, Tair Which ferritin subunit?
Tf, transferrin iron ion transport GO:0006826 IDA FB, Tair transport is inferred from radioactive Fe sequential colocalizing with location of each of the proteins in different parts of the duodenum
Tfrc, transferrin receptor iron ion transport GO:0006826 IDA FB, Tair Tfrc or Tfr2?
Tf, transferrin ferric iron transport GO:0015682 IDA RGD
ferritin ferric ion import GO:0033216 IDA SGD occurs_in UBERON:0000320 duodenal mucosa Which ferritin?
Tf, transferrin ferric ion import GO:0033216 IDA SGD occurs_in UBERON:0000320 duodenal mucosa
Tf, transferrin GO:0098706 -ferric iron import across plasma membrane IEP WB
Tfrc, transferrin receptor GO:0098706 -ferric iron import across plasma membrane IEP WB
ferritin iron ion homeostasis GO:0055072 IDA FB Which ferritin subunit?
Tf, transferrin iron ion homeostasis GO:0055072 IDA FB transport is inferred from radioactive Fe sequential colocalizing with location of each of the proteins in different parts of the duodenum
Tfrc, transferrin receptor iron ion homeostasis GO:0055072 IDA FB
ferritin, Fth1, Ftl1 GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0016512) lumen of duodenum
Tf, transferrin GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0016512)lumen of duodenum
Tfrc, transferrin receptor GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0002114) duodenum
Tf, transferrin GO:0050892 - intestinal absorption IEP WB has_input(ChEBI:29034) Maybe request "intestinal iron ion absorption".
Tfrc, transferrin receptor GO:0050892 - intestinal absorption IEP WB has_input(ChEBI:29034)
Tf, transferrin response to iron ion GO:0010039 IEP RGD movement between compartments dependent on iron level in diet
Tfrc, transferrin receptor response to iron ion GO:0010039 IEP RGD
human ferritin, FTH1 (UniProtKB:P02794), FTL (UniProtKB:P02792) GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0002114) duodenum
human TF (UniProtKB:P02787) GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0002114) duodenum
human TFRC (UniProtKB:P02786) GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0002114) duodenum
Cellular Component
Tf, transferrin cell tip GO:0051286 IDA RGD Figure 5 - ID, 15 min; text description
Tfrc, transferrin receptor cell surface GO:0009986 IDA RGD Figure 5; text description
Tfrc, transferrin receptor GO:0031528 - microvillus membrane IDA WB
Tf, transferrin, Fth1, Ftl1, ferritin GO:0005615 - extracellular space IDA WB
Molecular Function
Fth1, Ftl1, ferritin iron ion binding, GO:0005506 IDA FB, Tair, WB occurs_in UBERON:0000320 duodenal mucosa Which ferritin subunit?
Tf, transferrin iron ion binding, GO:0005506 IDA FB, Tair, WB occurs_in UBERON:0000320 duodenal mucosa
Tf, transferrin ferric iron binding GO:0008199 IDA RGD, SGD
ferritin ferric iron binding GO:0008199 IDA SGD Which ferritin?
Tfrc, transferrin receptor GO:0004998 - transferrin receptor activity IEP WB occurs_in(UBERON:0008346) duodenal epithelium IEP for MF annotation???

Minutes

  • On call: Alice, Barbara, Edith, Giulia, Helen, Kimberly, Li, Midori, Olivia, Paola, Paul T., Penelope, Petra, Sabrina, Sage, Stacia, Stan, Tanya, Val

Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016

  • Please register if you haven't already
  • Please check the meeting agenda to see what topics will be discussed
    • If you are interested in raising a topic for discussion, please add it along with your name and the amount of time you think will be needed

Annotation Consistency Exercise

  • Issues we discussed:
    • Determining what annotations could be made to ferritin
      • Authors used an antibody, but didn't say exactly what the antibody recognized and there are many different potential subunits to the rat ferritin complex (light and heavy chains)
    • Differences in evidence code usage
      • Most curators used IDA for the transport annotations, but there was also IEP
      • There was some discussion about use of IC to support annotations, as there didn't seem to be a single experiment that showed both iron binding and transport
    • Support for iron homeostasis annotations?
      • We discussed whether an iron homeostasis annotation added much if the proteins were already annotated to irton transport
      • Did the experiments simply show support for nutrient uptake or was there also support for homeostasis?
    • Annotations to intestinal absorption
      • Seems a broad, high level term to use, but could be made more specific with annotation extensions, e.g. has_input(ferric ion), or by requesting a new, more granular term like intestinal iron absoption.
      • For terms like intestinal iron absorption, the potential list of terms could get very long - is this necessary? Would an alternative term such as intestinal metal ion absorption be a reasonable alternative?
    • Additional papers with knock-down experiments might help to better support the Biological Process annotations
    • Cellular component annotations
      • What evidence is sufficient to annotate to cell surface vs a membrane term? Note that this issue has been raised before and will be discussed at the GOC meeting next month.
    • Molecular function annotations
      • What evidence would support the transferrin receptor activity annotation? Maybe IC, but not IEP.
  • Review of Noctua model:
    • Ferritin is represented in this model by the generic GO complex, so no specific annotations to a rat complex, or particular subunits, would be made
    • The model represents the relation between transferrin and the transferrin receptor as 'directly provides input for'
      • David was not certain that this was the best relation to use, but wanted to capture the idea that there was some sort of causal relation between the transferrin and the transferrin receptor that led to uptake into the epithelium
    • Note that it would be fine to use evidence from more than one paper to support a given LEGO model

Discussion of Outstanding github Tickets

  • We discussed two issues surrounding an ontology request for a new term maintenance of differentiated cell state
  • The first involved what is generally meant by 'maintenance of differentiation'
    • Would this term refer to a developmental process or program that specifically controls de-differentiation after a cell has fully differentiated and a change in its environment results in reversion to an undifferentiated state? Or, does this refer to a process that is simply part of differentiation?
    • What experiments would adequately demonstrate a distinction between these two?
  • The second involved what is meant by 'positive regulation of a process' and whether that includes the concept of maintenance of that process
    • The website guidelines on regulation specifically include 'maintenance', along with 'activation' and 'upregulation', of a process as positive regulation of that process - see http://geneontology.org/page/regulation
    • However, the existing term definitions for 'positive regulation of biological process' do not specifically state that this includes maintenance; they only refer to 'Any process that activates or increases the frequency, rate or extent of a biological process.' - see http://amigo.geneontology.org/amigo/term/GO:0048518
    • Should the definition of 'positive regulation of biological process' term (and its children) explicitly refer to maintenance as well as activation and induction?
    • Do we have examples of process maintenance that is considered regulation of that process?
    • Requested that this issue be added to an ontology editors call
Retrieved from "https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-10-25&oldid=62292"