Annotation Conf. Call 2016-08-23: Difference between revisions
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==Annotation Consistency Exercise== | ==Annotation Consistency Exercise== | ||
http://www.ncbi.nlm.nih.gov/pubmed/23246437 | http://www.ncbi.nlm.nih.gov/pubmed/23246437 | ||
some possible items to discuss: | |||
#when to include specific targets or not | |||
#which qualifier/RO term to use in col16 extensions | |||
#when col8 vs. col16 | |||
#new term chromosome_axis? | |||
#do people still make TAS/NAS annotations? | |||
#other topics? | |||
{| class="wikitable" border="1" | {| class="wikitable" border="1" | ||
Line 21: | Line 29: | ||
! With/From (col 8) | ! With/From (col 8) | ||
! Annotation Extension (col 16) | ! Annotation Extension (col 16) | ||
|- | |||
| SET1 | |||
| GO:1990837 sequence-specific double-stranded DNA binding | |||
| IMP | |||
| | |||
| has_direct_input SO:0000339 recombination_hotspot, happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SET1 | |||
| GO:0010844 recombination hotspot binding | |||
| IMP | |||
| | |||
| has_direct_input SO:0000955 double_stranded_DNA_chromosome, happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SET1 | |||
| GO:0051568 histone H3-K4 methylation | |||
| IDA | |||
| | |||
| | |||
|- | |||
| SET1 | |||
| GO:0044648 histone H3-K4 dimethylation | |||
| IMP | |||
| | |||
| | |||
|- | |- | ||
| SET1 | | SET1 | ||
Line 26: | Line 58: | ||
| IMP | | IMP | ||
| | | | ||
| positively_regulates GO:0042138: meiotic DNA double-strand break formation | |||
|- | |||
| SET1 | |||
| GO:0044648 histone H3-K4 dimethylation | |||
| IMP | |||
| | | | ||
| happens_during GO:0051321 meiotic cell cycle | |||
|- | |- | ||
| SET1 | | SET1 | ||
Line 39: | Line 77: | ||
| | | | ||
| | | | ||
|- | |||
| SET1 | |||
| GO:0080182 histone H3-K4 trimethylation | |||
| IMP | |||
| | |||
| happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SET1 | |||
| GO:0006279 premeiotic DNA replication | |||
| IMP | |||
| | |||
| happens_during GO:0051321 meiotic cell cycle | |||
|- | |- | ||
| SET1 | | SET1 | ||
Line 48: | Line 98: | ||
| SET1 | | SET1 | ||
| GO:1903341 regulation of meiotic DNA double-strand break formation | | GO:1903341 regulation of meiotic DNA double-strand break formation | ||
| IMP | |||
| | |||
| | |||
|- | |||
| SET1 | |||
| GO:1903341 regulation of meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SET1 | |||
| GO:1903343 positive regulation of meiotic DNA double-strand break formation | |||
| IDA | |||
| | |||
| | |||
|- | |||
| SET1 | |||
| GO:1903343 positive regulation of meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| occurs_at CYS3, BUD23, DEP1, LSB3 | |||
|- | |||
| SET1 | |||
| GO:1903343 positive regulation of meiotic DNA double-strand break formation | |||
| IGI | |||
| w/HHT1, HHT2 | |||
| | |||
|- | |||
| SET1 | |||
| GO:1903342 negative regulation of meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| occurs_at PES4, ARG3 | |||
|- | |||
| SET1 | |||
| GO:0010674 negative regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle | |||
| IMP | |||
| | |||
| regulates_expression_of PES4, ARG3 | |||
|- | |||
| SET1 | |||
| GO:0071168 protein localization to chromatin | |||
| IC | |||
| from/ GO:0000785 chromatin, GO:1903343 positive regulation of meiotic DNA double-strand break formation | |||
| has_input SPP1 | |||
|- | |||
| SET1 | |||
| GO:0071168 protein localization to chromatin | |||
| IMP | |||
| | |||
| occurs_at SO:0000502 transcribed region, has_inut SPP1, happens_during GO:0000278 mitotic cell cycle | |||
|- | |||
| SET1 | |||
| NTR NTR: chromosome axis | |||
| IMP | |||
| | |||
| happens_during GO:0051321 meiotic cell cycle, conincident_with SO:0000339 recombination_hotspot | |||
|- | |||
| SWD3 | |||
| GO:0051568 histone H3-K4 methylation | |||
| IMP | | IMP | ||
| | | | ||
Line 60: | Line 170: | ||
| SWD3 | | SWD3 | ||
| GO:0080182 histone H3-K4 trimethylation | | GO:0080182 histone H3-K4 trimethylation | ||
| IMP | |||
| | |||
| | |||
|- | |||
| SWD3 | |||
| GO:0044648 histone H3-K4 dimethylation | |||
| IMP | |||
| | |||
| positively_regulates GO:0042138: meiotic DNA double-strand break formation | |||
|- | |||
| SWD3 | |||
| GO:0080182 histone H3-K4 trimethylation | |||
| IMP | |||
| | |||
| positively_regulates GO:0042138: meiotic DNA double-strand break formation | |||
|- | |||
| SWD3 | |||
| GO:0051569 regulation of histone H3-K4 methylation | |||
| IMP | | IMP | ||
| | | | ||
Line 75: | Line 203: | ||
| | | | ||
| | | | ||
|- | |||
| SWD3 | |||
| GO:1903342 negative regulation of meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| occurs_at PES4, ARG3 | |||
|- | |||
| SWD3 | |||
| GO:1903343 positive regulation of meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| occurs_at CYS3, BUD23, DEP1, LSB3 | |||
|- | |- | ||
| SPP1 | | SPP1 | ||
Line 87: | Line 227: | ||
| | | | ||
| | | | ||
|- | |||
| SPP1 | |||
| GO:0044648 histone H3-K4 dimethylation | |||
| IMP | |||
| | |||
| positively_regulates GO:0042138: meiotic DNA double-strand break formation | |||
|- | |||
| SPP1 | |||
| GO:0080182 histone H3-K4 trimethylation | |||
| IMP | |||
| | |||
| positively_regulates GO:0042138: meiotic DNA double-strand break formation | |||
|- | |||
| SPP1 | |||
| GO:0051569 regulation of histone H3-K4 methylation | |||
| IMP | |||
| | |||
| | |||
|- | |||
| SPP1 | |||
| GO:0051571 positive regulation of histone H3-K4 methylation | |||
| IMP | |||
| | |||
| | |||
|- | |||
| SPP1 | |||
| GO:1903342 negative regulation of meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| occurs_at PES4, ARG3 | |||
|- | |||
| SPP1 | |||
| GO:1903343 positive regulation of meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| occurs_at CYS3, BUD23, DEP1, LSB3 | |||
|- | |- | ||
| SPP1 | | SPP1 | ||
Line 99: | Line 275: | ||
| | | | ||
| | | | ||
|- | |||
| SPP1 | |||
| GO:0003682 chromatin binding | |||
| IDA | |||
| | |||
| occurs_at SO:0000502 transcribed region, happens_during GO:0000278 mitotic cell cycle | |||
|- | |||
| SPP1 | |||
| GO:0005515 protein binding | |||
| IPI | |||
| w/REC107 (MER2) | |||
| happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SPP1 | |||
| GO:0005515 protein binding | |||
| IDA | |||
| | |||
| has_input REC107 (MER2), happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SPP1 | |||
| GO:0005515 protein binding | |||
| IPI | |||
| w/REC107 (MER2) | |||
| positively_regulates NTR: chromosome axis binding, happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SPP1 | |||
| GO:0030674 protein binding, bridging | |||
| IC | |||
| from GO:0005515 protein_binding, GO:0035064 methylated histone binding | |||
| happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SPP1 | |||
| GO:0035064 methylated histone binding | |||
| TAS | |||
| | |||
| occurs_at SO:0000170 RNA polymerase II promoter | |||
|- | |- | ||
| SPP1 | | SPP1 | ||
Line 117: | Line 329: | ||
| | | | ||
| has_direct_input SPO11, occurs_at GO:0035861 site of double-strand break | | has_direct_input SPO11, occurs_at GO:0035861 site of double-strand break | ||
|- | |||
| SPP1 | |||
| GO:1990166 protein localization to site of double-strand break | |||
| IMP | |||
| | |||
| transports_or_maintains_localization_of SPO11, happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SPP1 | |||
| GO:new regulation of protein localization to site of double-strand break | |||
| IMP | |||
| | |||
| has_regulation_target SPO11 | |||
|- | |- | ||
| SPP1 | | SPP1 | ||
Line 123: | Line 347: | ||
| | | | ||
| coincident_with SO:0000316 CDS | | coincident_with SO:0000316 CDS | ||
|- | |||
| SPP1 | |||
| GO:0000790 nuclear chromatin | |||
| IDA | |||
| | |||
| exists_during GO:0000278 mitotic cell cycle | |||
|- | |||
| SPP1 | |||
| GO:0000785 chromatin | |||
| IDA | |||
| | |||
| coincident_with RPS0A and ADH1, part_of CL:0000334 vegetative cell (sensu Fungi) | |||
|- | |||
| SPP1 | |||
| NTR NTR: chromosome axis | |||
| IDA | |||
| | |||
| happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SPP1 | |||
| GO:new chromosome axis | |||
| IDA | |||
| | |||
| exists_during GO:0051321 meiotic cell cycle | |||
|- | |- | ||
| SPP1 | | SPP1 | ||
Line 135: | Line 383: | ||
| | | | ||
| | | | ||
|- | |||
| SPP1 | |||
| GO:0048188 Set1C/COMPASS complex | |||
| NAS | |||
| | |||
| | |||
|- | |||
| REC107 (MER2) | |||
| GO:0005515 protein binding | |||
| IPI | |||
| w/SPP1 | |||
| happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| REC107 (MER2) | |||
| GO:0005515 protein binding | |||
| IDA | |||
| | |||
| has_input SPP1, happens_during GO:0051321 meiotic cell cycle | |||
|- | |||
| REC107 (MER2) | |||
| GO:0005515 protein binding | |||
| IPI | |||
| w/SPP1 | |||
| positively_regulates NTR: chromosome axis binding, happens_during GO:0051321 meiotic cell cycle | |||
|- | |- | ||
| REC107 (MER2) | | REC107 (MER2) | ||
Line 141: | Line 413: | ||
| | | | ||
| happens_during GO:0051321 meiotic cell cycle, has_direct_input SPP1, occurs_at GO:NTR chromosome axis | | happens_during GO:0051321 meiotic cell cycle, has_direct_input SPP1, occurs_at GO:NTR chromosome axis | ||
|- | |||
| REC107 (MER2) | |||
| GO:0042138 meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| | |||
|- | |- | ||
| REC107 (MER2) | | REC107 (MER2) | ||
Line 147: | Line 425: | ||
| | | | ||
| exists_during GO:0051321 meiotic cell cycle | | exists_during GO:0051321 meiotic cell cycle | ||
|- | |||
| REC104 | |||
| GO:0042138 meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| | |||
|- | |||
| REC102 | |||
| GO:0042138 meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| | |||
|- | |||
| REC114 | |||
| GO:0042138 meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| | |||
|- | |||
| MEI4 | |||
| GO:0042138 meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| | |||
|- | |||
| SKI8 | |||
| GO:0042138 meiotic DNA double-strand break formation | |||
| IMP | |||
| | |||
| | |||
|- | |- | ||
| SPO11 | | SPO11 | ||
Line 153: | Line 461: | ||
| | | | ||
| | | | ||
|- | |||
| SPO11 | |||
| GO:0035861 site of double-strand break | |||
| IDA | |||
| | |||
| exists_during GO:0051321 meiotic cell cycle | |||
|- | |||
| SPO11 | |||
| GO:0035861 site of double-strand break | |||
| IDA | |||
| | |||
| happens_during GO:0051321 meiotic cell cycle | |||
|- | |- | ||
|} | |} | ||
Noctua model: http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001783?barista_token=lyg8ba4blv2702bcpp9a# | |||
=Minutes= | |||
*On call: Alice, Barbara, David H., David OS, Edith, Elena, George, Giulia, Helen, Kimberly, Li, Melanie, Moni, Paola, Penelope, Petra, Ruth, Sage, Shur-Jen, Stacia, Tanya | |||
==Upcoming Meetings== | |||
===Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016=== | |||
*Please add your name to the attendees list on the logistics wiki page | |||
*Please also indicate if you are planning to stay for the Noctua/LEGO training session on Monday, 11/7, the day after the consortium meeting ends | |||
===UK LEGO/Noctua Training=== | |||
*Need full list of attendees on the logistics page - DONE | |||
*Off-site people need to make sure that Claire has given your name to EBI security | |||
==Annotation Consistency Exercise== | |||
===Overall Consistency=== | |||
*Generally our annotations of the biology were consistent, but there are still issues with annotating to the process term or regulation of that process - this goes back to the perennial issue of defining when a process begins and ends | |||
===LEGO Modeling and Use of Regulates Relations=== | |||
*There is a LEGO model in progress for this paper (see link above) | |||
*Note that when annotating in LEGO, regulation (usually known to be positive or negative) is captured as a relation between the MF and the BP - curators would not enter a regulation BP term as the process | |||
**How will the correct annotations to 'regulation of BP' be output in the legacy GAF/GPAD files then? | |||
**The reasoner that is used to generate the GAF/GPAD files would be used to make the correct BP annotations using the existing relations | |||
===Including Targets as Annotation Extensions=== | |||
*There was also some discussion on when to include targets of a process - no clear decision or guideline there yet | |||
===Protein Binding - IPI and With/From or IDA and Annotation Extensions?=== | |||
*Another big issue of discussion was how to represent protein binding - Col. 8 (With/From) vs Col. 16 (Annotation Extension) | |||
**Historically, we have used the IPI evidence code and Col. 8 to capture the identifier of the interacting gene product, but LEGO handles this is a different way, by using the IDA evidence code and 'has_input' relation which is translated into a Col. 16 annotation | |||
**Using Col. 16 to capture protein binding interactors is not a new idea; Emily proposed this several years ago | |||
**Protein binding assays are direct assays, so that is not inconsistent with using that evidence code, which we already use when the exact identifier of the interacting partner is not known (e.g. actin) | |||
**Using Col. 16 might allow us to more readily create 'x protein family binding' terms | |||
**Ruth pointed out, though, that there are downstream implications to making this change that need to be sorted out first | |||
***First, no system currently exists for automatically creating these 'x protein family binding' terms, so that is not an issue at this point | |||
***Second, we would need a system in place to handle the transition for existing annotations BEFORE we make this switch | |||
****This system would need to handle cross-species experiments (we should review these types of experiments in LEGO, too) | |||
***This, Tony S. and Ruth worked on a project that would translate GO's protein binding IPI annotations into a Cytoscape view of protein binding networks; this would need to be changed to accommodate the new representation | |||
*For now, though, we will continue to use IPI and the With/From column if the identifier is known, and IDA with nothing in the With/From column if the identifier is not known | |||
*AI: Assess necessary steps to make the change from With/From to AEs for protein binding | |||
===New CC Term - Chromosome Axis=== | |||
*One of the reasons Stacia picked this paper was to explore the idea of creating a new CC term: 'chromosome axis' | |||
*Is this a real CC? If so, how would it be defined? | |||
*The chromosome axis appears to be part of a temporary arrangement of the meiotic chromosome | |||
**Does the impermanent nature of this structure make it unsuitable for a GO CC term? | |||
*The concept of the chromosome axis does appear important for understanding the biology of meiotic recombination, though | |||
*AI: Attempt a definition of chromosome axis term and consult with authors of this paper or other experts in the field for feedback on term, definition, and ontology placemnt | |||
===Clarification on Pipes and Commas in Annotation Extensions=== | |||
*Just a note - targets captured in annotation extensions should be separated with a pipe if they are acted upon individually | |||
*The use of a comma in the table for this exercise is just an artifact of wiki formatting that creates a new cell in the wiki table | |||
[[Category: Annotation Working Group]] | [[Category: Annotation Working Group]] |
Latest revision as of 11:46, 25 August 2016
Bluejeans URL: https://bluejeans.com/993661940
Agenda
Upcoming Meetings
Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016
- Please indicate on the Meeting Logistics Page if you plan to come.
- We are now planning 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.
UK LEGO/Noctua Training
- There will be a LEGO/Noctua training session in Hinxton, UK from Wednesday, 8/31 - Friday, 9/2.
- Logistics
- Agenda
Annotation Consistency Exercise
http://www.ncbi.nlm.nih.gov/pubmed/23246437
some possible items to discuss:
- when to include specific targets or not
- which qualifier/RO term to use in col16 extensions
- when col8 vs. col16
- new term chromosome_axis?
- do people still make TAS/NAS annotations?
- other topics?
Gene Name (col 2) | GO ID and term name (col 5) | Evidence (col 7) | With/From (col 8) | Annotation Extension (col 16) |
---|---|---|---|---|
SET1 | GO:1990837 sequence-specific double-stranded DNA binding | IMP | has_direct_input SO:0000339 recombination_hotspot, happens_during GO:0051321 meiotic cell cycle | |
SET1 | GO:0010844 recombination hotspot binding | IMP | has_direct_input SO:0000955 double_stranded_DNA_chromosome, happens_during GO:0051321 meiotic cell cycle | |
SET1 | GO:0051568 histone H3-K4 methylation | IDA | ||
SET1 | GO:0044648 histone H3-K4 dimethylation | IMP | ||
SET1 | GO:0044648 histone H3-K4 dimethylation | IMP | positively_regulates GO:0042138: meiotic DNA double-strand break formation | |
SET1 | GO:0044648 histone H3-K4 dimethylation | IMP | happens_during GO:0051321 meiotic cell cycle | |
SET1 | GO:0080182 histone H3-K4 trimethylation | IDA | ||
SET1 | GO:0080182 histone H3-K4 trimethylation | IMP | ||
SET1 | GO:0080182 histone H3-K4 trimethylation | IMP | happens_during GO:0051321 meiotic cell cycle | |
SET1 | GO:0006279 premeiotic DNA replication | IMP | happens_during GO:0051321 meiotic cell cycle | |
SET1 | GO:0010780 meiotic DNA double-strand break formation | IMP | ||
SET1 | GO:1903341 regulation of meiotic DNA double-strand break formation | IMP | ||
SET1 | GO:1903341 regulation of meiotic DNA double-strand break formation | IMP | happens_during GO:0051321 meiotic cell cycle | |
SET1 | GO:1903343 positive regulation of meiotic DNA double-strand break formation | IDA | ||
SET1 | GO:1903343 positive regulation of meiotic DNA double-strand break formation | IMP | occurs_at CYS3, BUD23, DEP1, LSB3 | |
SET1 | GO:1903343 positive regulation of meiotic DNA double-strand break formation | IGI | w/HHT1, HHT2 | |
SET1 | GO:1903342 negative regulation of meiotic DNA double-strand break formation | IMP | occurs_at PES4, ARG3 | |
SET1 | GO:0010674 negative regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle | IMP | regulates_expression_of PES4, ARG3 | |
SET1 | GO:0071168 protein localization to chromatin | IC | from/ GO:0000785 chromatin, GO:1903343 positive regulation of meiotic DNA double-strand break formation | has_input SPP1 |
SET1 | GO:0071168 protein localization to chromatin | IMP | occurs_at SO:0000502 transcribed region, has_inut SPP1, happens_during GO:0000278 mitotic cell cycle | |
SET1 | NTR NTR: chromosome axis | IMP | happens_during GO:0051321 meiotic cell cycle, conincident_with SO:0000339 recombination_hotspot | |
SWD3 | GO:0051568 histone H3-K4 methylation | IMP | ||
SWD3 | GO:0044648 histone H3-K4 dimethylation | IMP | ||
SWD3 | GO:0080182 histone H3-K4 trimethylation | IMP | ||
SWD3 | GO:0044648 histone H3-K4 dimethylation | IMP | positively_regulates GO:0042138: meiotic DNA double-strand break formation | |
SWD3 | GO:0080182 histone H3-K4 trimethylation | IMP | positively_regulates GO:0042138: meiotic DNA double-strand break formation | |
SWD3 | GO:0051569 regulation of histone H3-K4 methylation | IMP | ||
SWD3 | GO:0010780 meiotic DNA double-strand break formation | IMP | ||
SWD3 | GO:1903341 regulation of meiotic DNA double-strand break formation | IMP | ||
SWD3 | GO:1903342 negative regulation of meiotic DNA double-strand break formation | IMP | occurs_at PES4, ARG3 | |
SWD3 | GO:1903343 positive regulation of meiotic DNA double-strand break formation | IMP | occurs_at CYS3, BUD23, DEP1, LSB3 | |
SPP1 | GO:0044648 histone H3-K4 dimethylation | IMP | ||
SPP1 | GO:0080182 histone H3-K4 trimethylation | IMP | ||
SPP1 | GO:0044648 histone H3-K4 dimethylation | IMP | positively_regulates GO:0042138: meiotic DNA double-strand break formation | |
SPP1 | GO:0080182 histone H3-K4 trimethylation | IMP | positively_regulates GO:0042138: meiotic DNA double-strand break formation | |
SPP1 | GO:0051569 regulation of histone H3-K4 methylation | IMP | ||
SPP1 | GO:0051571 positive regulation of histone H3-K4 methylation | IMP | ||
SPP1 | GO:1903342 negative regulation of meiotic DNA double-strand break formation | IMP | occurs_at PES4, ARG3 | |
SPP1 | GO:1903343 positive regulation of meiotic DNA double-strand break formation | IMP | occurs_at CYS3, BUD23, DEP1, LSB3 | |
SPP1 | GO:NTR chromosome axis | IDA | happens_during GO:0051321 meiotic cell cycle | |
SPP1 | GO:0003682 chromatin binding | IDA | ||
SPP1 | GO:0003682 chromatin binding | IDA | occurs_at SO:0000502 transcribed region, happens_during GO:0000278 mitotic cell cycle | |
SPP1 | GO:0005515 protein binding | IPI | w/REC107 (MER2) | happens_during GO:0051321 meiotic cell cycle |
SPP1 | GO:0005515 protein binding | IDA | has_input REC107 (MER2), happens_during GO:0051321 meiotic cell cycle | |
SPP1 | GO:0005515 protein binding | IPI | w/REC107 (MER2) | positively_regulates NTR: chromosome axis binding, happens_during GO:0051321 meiotic cell cycle |
SPP1 | GO:0030674 protein binding, bridging | IC | from GO:0005515 protein_binding, GO:0035064 methylated histone binding | happens_during GO:0051321 meiotic cell cycle |
SPP1 | GO:0035064 methylated histone binding | TAS | occurs_at SO:0000170 RNA polymerase II promoter | |
SPP1 | GO:0010780 meiotic DNA double-strand break formation | IMP | ||
SPP1 | GO:1903341 regulation of meiotic DNA double-strand break formation | IMP | ||
SPP1 | GO:0034613 cellular protein localization | IMP | has_direct_input SPO11, occurs_at GO:0035861 site of double-strand break | |
SPP1 | GO:1990166 protein localization to site of double-strand break | IMP | transports_or_maintains_localization_of SPO11, happens_during GO:0051321 meiotic cell cycle | |
SPP1 | GO:new regulation of protein localization to site of double-strand break | IMP | has_regulation_target SPO11 | |
SPP1 | GO:0000790 nuclear chromatin | IDA | coincident_with SO:0000316 CDS | |
SPP1 | GO:0000790 nuclear chromatin | IDA | exists_during GO:0000278 mitotic cell cycle | |
SPP1 | GO:0000785 chromatin | IDA | coincident_with RPS0A and ADH1, part_of CL:0000334 vegetative cell (sensu Fungi) | |
SPP1 | NTR NTR: chromosome axis | IDA | happens_during GO:0051321 meiotic cell cycle | |
SPP1 | GO:new chromosome axis | IDA | exists_during GO:0051321 meiotic cell cycle | |
SPP1 | GO:new [condensed?] chromosome axis | IDA | exists_during GO:0051321 meiotic cell cycle | |
SPP1 | NOT GO:0035861 site of double-strand break | IDA | ||
SPP1 | GO:0048188 Set1C/COMPASS complex | NAS | ||
REC107 (MER2) | GO:0005515 protein binding | IPI | w/SPP1 | happens_during GO:0051321 meiotic cell cycle |
REC107 (MER2) | GO:0005515 protein binding | IDA | has_input SPP1, happens_during GO:0051321 meiotic cell cycle | |
REC107 (MER2) | GO:0005515 protein binding | IPI | w/SPP1 | positively_regulates NTR: chromosome axis binding, happens_during GO:0051321 meiotic cell cycle |
REC107 (MER2) | GO:0034613 cellular protein localization | IMP | happens_during GO:0051321 meiotic cell cycle, has_direct_input SPP1, occurs_at GO:NTR chromosome axis | |
REC107 (MER2) | GO:0042138 meiotic DNA double-strand break formation | IMP | ||
REC107 (MER2) | GO:new [condensed?] chromosome axis | IDA | exists_during GO:0051321 meiotic cell cycle | |
REC104 | GO:0042138 meiotic DNA double-strand break formation | IMP | ||
REC102 | GO:0042138 meiotic DNA double-strand break formation | IMP | ||
REC114 | GO:0042138 meiotic DNA double-strand break formation | IMP | ||
MEI4 | GO:0042138 meiotic DNA double-strand break formation | IMP | ||
SKI8 | GO:0042138 meiotic DNA double-strand break formation | IMP | ||
SPO11 | GO:0035861 site of double-strand break | IDA | ||
SPO11 | GO:0035861 site of double-strand break | IDA | exists_during GO:0051321 meiotic cell cycle | |
SPO11 | GO:0035861 site of double-strand break | IDA | happens_during GO:0051321 meiotic cell cycle |
Noctua model: http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001783?barista_token=lyg8ba4blv2702bcpp9a#
Minutes
- On call: Alice, Barbara, David H., David OS, Edith, Elena, George, Giulia, Helen, Kimberly, Li, Melanie, Moni, Paola, Penelope, Petra, Ruth, Sage, Shur-Jen, Stacia, Tanya
Upcoming Meetings
Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016
- Please add your name to the attendees list on the logistics wiki page
- Please also indicate if you are planning to stay for the Noctua/LEGO training session on Monday, 11/7, the day after the consortium meeting ends
UK LEGO/Noctua Training
- Need full list of attendees on the logistics page - DONE
- Off-site people need to make sure that Claire has given your name to EBI security
Annotation Consistency Exercise
Overall Consistency
- Generally our annotations of the biology were consistent, but there are still issues with annotating to the process term or regulation of that process - this goes back to the perennial issue of defining when a process begins and ends
LEGO Modeling and Use of Regulates Relations
- There is a LEGO model in progress for this paper (see link above)
- Note that when annotating in LEGO, regulation (usually known to be positive or negative) is captured as a relation between the MF and the BP - curators would not enter a regulation BP term as the process
- How will the correct annotations to 'regulation of BP' be output in the legacy GAF/GPAD files then?
- The reasoner that is used to generate the GAF/GPAD files would be used to make the correct BP annotations using the existing relations
Including Targets as Annotation Extensions
- There was also some discussion on when to include targets of a process - no clear decision or guideline there yet
Protein Binding - IPI and With/From or IDA and Annotation Extensions?
- Another big issue of discussion was how to represent protein binding - Col. 8 (With/From) vs Col. 16 (Annotation Extension)
- Historically, we have used the IPI evidence code and Col. 8 to capture the identifier of the interacting gene product, but LEGO handles this is a different way, by using the IDA evidence code and 'has_input' relation which is translated into a Col. 16 annotation
- Using Col. 16 to capture protein binding interactors is not a new idea; Emily proposed this several years ago
- Protein binding assays are direct assays, so that is not inconsistent with using that evidence code, which we already use when the exact identifier of the interacting partner is not known (e.g. actin)
- Using Col. 16 might allow us to more readily create 'x protein family binding' terms
- Ruth pointed out, though, that there are downstream implications to making this change that need to be sorted out first
- First, no system currently exists for automatically creating these 'x protein family binding' terms, so that is not an issue at this point
- Second, we would need a system in place to handle the transition for existing annotations BEFORE we make this switch
- This system would need to handle cross-species experiments (we should review these types of experiments in LEGO, too)
- This, Tony S. and Ruth worked on a project that would translate GO's protein binding IPI annotations into a Cytoscape view of protein binding networks; this would need to be changed to accommodate the new representation
- For now, though, we will continue to use IPI and the With/From column if the identifier is known, and IDA with nothing in the With/From column if the identifier is not known
- AI: Assess necessary steps to make the change from With/From to AEs for protein binding
New CC Term - Chromosome Axis
- One of the reasons Stacia picked this paper was to explore the idea of creating a new CC term: 'chromosome axis'
- Is this a real CC? If so, how would it be defined?
- The chromosome axis appears to be part of a temporary arrangement of the meiotic chromosome
- Does the impermanent nature of this structure make it unsuitable for a GO CC term?
- The concept of the chromosome axis does appear important for understanding the biology of meiotic recombination, though
- AI: Attempt a definition of chromosome axis term and consult with authors of this paper or other experts in the field for feedback on term, definition, and ontology placemnt
Clarification on Pipes and Commas in Annotation Extensions
- Just a note - targets captured in annotation extensions should be separated with a pipe if they are acted upon individually
- The use of a comma in the table for this exercise is just an artifact of wiki formatting that creates a new cell in the wiki table