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

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*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==
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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
|-
|-
|''Cellular Component''
| ferritin
|-
| iron ion transport GO:0006826
| gene
| IDA
|
| FB, Tair
| GOID term
| evidence code
|
|
| comment
|-
|
|
|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
| Which ferritin subunit?
|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''
|-  
|-  
|-
| Tf, transferrin
| gflB
| iron ion transport GO:0006826
|
| GO:0005737 cytoplasm
| IDA
| IDA
|  
| FB, Tair
|
|
| unstimulated cells
| transport is inferred from radioactive Fe sequential colocalizing with location of each of the proteins in different parts of the duodenum
|-
|-
| gflB
| Tfrc, transferrin receptor
|
| iron ion transport GO:0006826
| GO:1904269 cell leading edge cell cortex
| IDA
| IDA
| FB, Tair
|
|
|
| Tfrc or Tfr2?
| unstimulated cells
|-
|-
| gflB
| Tf, transferrin
|
| ferric iron transport GO:0015682
| GO:0005938 cell cortex
| IDA
| IDA
| RGD
|
|
| 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
| ferritin
|
| ferric ion import GO:0033216
| GO:0005737 cytoplasm
| IDA
| IDA
|
| SGD
|
|occurs_in UBERON:0000320 duodenal mucosa
| 5a
| Which ferritin?
|-
|-  
| gflB
| Tf, transferrin
|
| ferric ion import GO:0033216
| GO:0005737 cytoplasm
| IDA
| IDA
|
| SGD
| exists_during asexual reproduction
|occurs_in UBERON:0000320 duodenal mucosa
|
|  
|-
|-
| gflB
| Tf, transferrin
|
| GO:0098706 -ferric iron import across plasma membrane
| GO:0005938 cell cortex
| IEP
| IDA
| WB
|
| exists_during response to cAMP
|
|
|
|-
|-
| gflB
| Tfrc, transferrin receptor
| GO:0098706 -ferric iron import across plasma membrane
| IEP
| WB
|
|
| GO:0031252 cell leading edge
| IDA
|
| exists_during chemotaxis to cAMP
|
|
|-
|-
| gflB
| ferritin
|
| iron ion homeostasis GO:0055072
| GO:0005886 plasma membrane
| IDA
| IDA
| FB
|
|
| exists_during chemotaxis to cAMP
| Which ferritin subunit?
|  annotated 'plasma membrane' because of latA + domain expression experiments, also Supp Fig. 5A shows Phospholipid binding (see MF)
|-  
|-
| Tf, transferrin
| GflB
| iron ion homeostasis GO:0055072
|
| GO:0005938 cell cortex
| IDA
| IDA
| FB
|
|
|
| transport is inferred from radioactive Fe sequential colocalizing with location of each of the proteins in different parts of the duodenum
|
|-
|-
| GflB
| Tfrc, transferrin receptor
|
| iron ion homeostasis GO:0055072
| GO:0031252 cell leading edge
| IDA
| IDA
| FB
|
|
| exists_during chemotaxis (GO:0006935)
|  
|
|-
|-
| gflB
| ferritin, Fth1, Ftl1
|
| GO:0060586 - multicellular organismal iron ion homeostasis
| GO:0005737 cytoplasm
| IEP
| IDA
| WB
|
| occurs_in(UBERON:0000320) duodenal mucosa|occurs_in(UBERON:0016512) lumen of duodenum
|
|
| pg 462 right column
|-
| Tf, transferrin
| GO:0060586 - multicellular organismal iron ion homeostasis
| IEP
| WB
| occurs_in(UBERON:0016512)lumen of duodenum
|  
|-
|-
| gflB
| Tfrc, transferrin receptor
| GO:0060586 - multicellular organismal iron ion homeostasis
| IEP
| WB
| occurs_in(UBERON:0002114) duodenum
|
|
| GO:0031252 cell leading edge
|-
| IDA
| Tf, transferrin
|
| GO:0050892 - intestinal absorption
| exists during: cell chemotaxis GO:0060326
| IEP
| gradient treatment to induce chemotaxis; pg 462 right column
| WB
| has_input(ChEBI:29034)
| Maybe request "intestinal iron ion absorption".
|-
|-
| gflB
| Tfrc, transferrin receptor
| GO:0050892 - intestinal absorption
| IEP
| WB
| has_input(ChEBI:29034)
|
|
| GO:0005938 cell cortex
|-
| IDA
| Tf, transferrin
|
| response to iron ion GO:0010039
| happens during: cellular response to cAMP GO:0071320
| IEP
| uniform or global treatment with cAMP; pg 462 right column
| RGD
|  
| movement between compartments dependent on iron level in diet
|-
|-
| gflB
| Tfrc, transferrin receptor
|
| response to iron ion GO:0010039
| GO:0031256 leading edge membrane
| IEP
| IDA
| 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
|
|-
|-
| gflB
!''Cellular Component''
|
|-
| GO:0031252 cell leading edge
| Tf, transferrin
| cell tip GO:0051286
| IDA
| IDA
|
| RGD
|
|  
|
| Figure 5 - ID, 15 min; text description
|-
|-
| gflB
| Tfrc, transferrin receptor
|
| cell surface GO:0009986
| GO:1904269  cell leading edge cell cortex
| IDA
| IDA
| RGD
|
|
| localization_dependent_on ?Galpha2
| Figure 5; text description
| requires binding of active Galpha
|-  
|-
| Tfrc, transferrin receptor
| Raf1
| GO:0031528 - microvillus membrane
|
| GO:1904269 cell leading edge cell cortex
| IDA
| IDA
|
| WB
|
|  
|
|  
|-
|-
| Ral
| Tf, transferrin, Fth1, Ftl1, ferritin
|
| GO:0005615 - extracellular space
| GO:1904269 cell leading edge cell cortex
| IDA
| IDA
|
| WB
|
|  
|
|  
|-
|-
| Rap1
!''Molecular Function''
|
| GO:0009279 cell outer membrane
| IDA
|
|
|
|-
|-
| Rap1
| Fth1, Ftl1, ferritin
|
| iron ion binding, GO:0005506
| GO:0005886 plasma membrane
| IDA
| IDA
|
| FB, Tair, WB
|
| occurs_in UBERON:0000320 duodenal mucosa
|
| Which ferritin subunit?
|-
|-
| rapA
| Tf, transferrin
|
| iron ion binding, GO:0005506
| GO:0005886 plasma membrane
| IDA
| IDA
| FB, Tair, WB
| occurs_in UBERON:0000320 duodenal mucosa
|
|
|
| 3a
|-
|-
| rapA
| Tf, transferrin
|
| ferric iron binding GO:0008199
| GO:0005886 plasma membrane
| IDA
| IDA
|
| RGD, SGD
|
|  
|
|
|-
|-
| rasG
| ferritin
|
| ferric iron binding GO:0008199
| GO:0005886 plasma membrane
| IDA
| IDA
|
| SGD
|
|  
| 3a
| Which ferritin?
|-
| RasG
|
| GO:0005886 plasma membrane
| IDA
|
|
|
|-
| RasG
|
| GO:0009279 cell outer membrane
| IDA
|
|
|
|-
|-
| RasG
| Tfrc, transferrin receptor
|
| GO:0004998 - transferrin receptor activity
| GO:0005886 plasma membrane
| IEP
| IDA
| WB
|
| occurs_in(UBERON:0008346) duodenal epithelium
|
| IEP for MF annotation???
|
|}
|}


=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
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