Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Map APO entities to OBA / GO (or whatever else) #928

Open
Tracked by #1
matentzn opened this issue Jan 30, 2024 · 5 comments
Open
Tracked by #1

Map APO entities to OBA / GO (or whatever else) #928

matentzn opened this issue Jan 30, 2024 · 5 comments
Assignees
@rays22

Comments

@matentzn
Copy link
Collaborator

matentzn commented Jan 30, 2024 •
edited
Loading

Related issues:

affected_entity_1_super affected_entity_1_super_name
APO:0000087 resistance to chemicals
APO:0000110 competitive fitness
APO:0000095 chemical compound accumulation
APO:0000082 osmotic stress resistance
APO:0000028 invasive growth
APO:0000147 heat sensitivity
APO:0000144 telomere length
APO:0000102 respiratory metabolism
APO:0000071 cytokinesis
APO:0000039 meiosis
APO:0000106 vegetative growth
APO:0000308 fermentative growth
APO:0000195 gamma ray resistance
APO:0000056 bud neck morphology
APO:0000041 sporulation
APO:0000212 bud morphology
APO:0000253 cell cycle progression
APO:0000200 budding pattern
APO:0000051 cell shape
APO:0000310 growth in exponential phase
APO:0000046 silencing
APO:0000143 chromosome/plasmid maintenance
APO:0000047 transposable element transposition
APO:0000199 chitin deposition
APO:0000209 protein/peptide distribution
APO:0000193 resistance to enzymatic treatment
APO:0000202 alkaline pH resistance
APO:0000205 ionic stress resistance
APO:0000075 endocytosis
APO:0000148 cold sensitivity
APO:0000198 mutation frequency
APO:0000098 utilization of carbon source
APO:0000099 utilization of nitrogen source
APO:0000309 respiratory growth
APO:0000085 UV resistance
APO:0000079 vacuolar transport
APO:0000125 utilization of phosphorus source
APO:0000316 chronological lifespan
APO:0000215 toxin resistance
APO:0000059 vacuolar morphology
APO:0000131 protein/peptide modification
APO:0000118 nuclear position
APO:0000196 mating type switching
APO:0000129 protein transport
APO:0000090 metal resistance
APO:0000149 protein/peptide accumulation
APO:0000083 oxidative stress resistance
APO:0000201 acid pH resistance
APO:0000130 small molecule transport
APO:0000050 cellular morphology
APO:0000312 cell death
APO:0000027 filamentous growth
APO:0000078 protein secretion
APO:0000042 spore germination
APO:0000208 chromosome segregation
APO:0000055 mitochondrial morphology
APO:0000204 hyperosmotic stress resistance
APO:0000159 biofilm formation
APO:0000065 flocculation
APO:0000081 killer toxin resistance
APO:0000197 colony sectoring
APO:0000120 actin cytoskeleton morphology
APO:0000242 lipid particle morphology
APO:0000043 spore wall formation
APO:0000105 mitochondrial genome maintenance
APO:0000052 cell size
APO:0000124 pheromone-induced cell cycle arrest
APO:0000029 pseudohyphal growth
APO:0000255 cell cycle progression in G1 phase
APO:0000111 viability
APO:0000096 nutrient utilization
APO:0000030 lifespan
APO:0000022 protein activity
APO:0000157 utilization of iron source
APO:0000127 nuclear export
APO:0000091 starvation resistance
APO:0000334 innate thermotolerance
APO:0000326 desiccation resistance
APO:0000307 anaerobic growth
APO:0000225 mitotic recombination
APO:0000128 peroxisomal transport
APO:0000044 sporulation efficiency
APO:0000224 RNA accumulation
APO:0000089 budding index
APO:0000080 stress resistance
APO:0000317 replicative lifespan
APO:0000213 spindle morphology
APO:0000064 liquid culture appearance
APO:0000037 pheromone sensitivity
APO:0000333 acquired thermotolerance
APO:0000040 meiotic recombination
APO:0000141 critical cell size at START (G1 cell-size checkpoint)
APO:0000155 apoptosis
APO:0000034 mating efficiency
APO:0000257 cell cycle progression through the G2/M phase transition
APO:0000101 fermentative metabolism
APO:0000109 survival rate in stationary phase
APO:0000032 mating response
APO:0000086 X ray resistance
APO:0000038 shmoo formation
APO:0000123 recovery from pheromone-induced cell cycle arrest
APO:0000074 autophagy
APO:0000025 axial budding pattern
APO:0000072 mitotic cell cycle
APO:0000077 nuclear transport
APO:0000220 necrotic cell death
APO:0000024 budding
APO:0000219 utilization of sulfur source
APO:0000061 colony color
APO:0000222 chemical compound excretion
APO:0000221 septum formation
APO:0000100 nutrient uptake
APO:0000214 position of spindle pole body
APO:0000058 peroxisomal morphology
APO:0000057 nuclear morphology
APO:0000271 RNA modification
APO:0000223 mating projection morphology
APO:0000239 pexophagy
APO:0000335 size of nucleolus
APO:0000240 mitophagy
APO:0000063 colony size
APO:0000126 nuclear import
APO:0000132 RNA localization
APO:0000053 cell wall morphology
APO:0000226 subcellular morphology
APO:0000276 prion formation
APO:0000060 colony appearance
APO:0000303 endomembrane system morphology
APO:0000054 cytoskeleton morphology
APO:0000299 vacuolar distribution
APO:0000036 pheromone production
APO:0000266 cell cycle progression in S phase
APO:0000104 mitochondrial rho- mutation frequency
APO:0000258 cell cycle progression in M phase
APO:0000026 bipolar budding pattern
APO:0000254 cell cycle progression in G2 phase
APO:0000269 cell cycle progression through the G1/S phase transition
APO:0000033 cell fusion
APO:0000264 cell cycle progression in metaphase
APO:0000035 nuclear fusion during mating
APO:0000337 polyploidy
APO:0000270 endoplasmic reticulum morphology
APO:0000076 mitochondrial transport
APO:0000327 hydrostatic pressure resistance
APO:0000259 cell cycle passage through the metaphase-anaphase transition
APO:0000277 prion loss
APO:0000218 redox state
APO:0000273 nucleolar morphology
APO:0000062 colony shape
APO:0000154 petite-negative
APO:0000145 oxidative phosphorylation
APO:0000241 freeze-thaw resistance
APO:0000048 virulence
APO:0000262 cell cycle progression in mid anaphase
APO:0000260 cell cycle progression in anaphase
APO:0000267 entry into G0 (stationary phase)
APO:0000302 vesicle distribution
APO:0000119 size of nucleus
APO:0000298 peroxisomal distribution
APO:0000315 plasma membrane morphology
APO:0000243 Golgi morphology
APO:0000297 mitochondrial distribution
APO:0000339 ribophagy
APO:0000194 ionizing radiation resistance
APO:0000288 adhesion
APO:0000336 aneuploidy
APO:0000092 temperature sensitive growth
APO:0000300 endoplasmic reticulum distribution
APO:0000203 hypoosmotic stress resistance
APO:0000301 Golgi distribution
APO:0000265 cell cycle progression in telophase
APO:0000342 late nucleophagy
APO:0000341 nucleophagy
APO:0000340 reticulophagy
APO:0000268 exit from G0 (stationary phase)
APO:0000216 fitness
APO:0000093 thermotolerance
APO:0000256 cell cycle passage through START
APO:0000084 radiation resistance
APO:0000274 prion state
APO:0000275 prion inheritance
APO:0000263 cell cycle progression in late anaphase
APO:0000073 intracellular transport
APO:0000338 micronucleophagy
@matentzn matentzn mentioned this issue Jan 30, 2024
Open
2 tasks
@rays22 rays22 self-assigned this Jan 30, 2024
@rays22
Copy link
Contributor

rays22 commented Jan 30, 2024 •
edited
Loading

Related issue: Map APO modifiers to PATO -- issue #927

@srengel
Copy link

srengel commented Feb 20, 2024 •
edited
Loading

Hi @matentzn @rays22 we have completed a first pass of splitting the APO terms into trait and process. we have done a first pass to assign process terms from GO. please take a look and let us know what you think.

APO_ID APO term trait? GO_ID GO_term_name type of synonym
APO:0000193 resistance to enzymatic treatment trait      
APO:0000050 cellular morphology trait      
APO:0000051 cell shape trait      
APO:0000052 cell size trait      
APO:0000053 cell wall morphology trait      
APO:0000054 cytoskeleton morphology trait      
APO:0000055 mitochondrial morphology trait      
APO:0000056 bud neck morphology trait      
APO:0000057 nuclear morphology trait      
APO:0000058 peroxisomal morphology trait      
APO:0000059 vacuolar morphology trait      
APO:0000060 colony appearance trait      
APO:0000061 colony color trait      
APO:0000062 colony shape trait      
APO:0000063 colony size trait      
APO:0000064 liquid culture appearance trait      
APO:0000089 budding index trait      
APO:0000118 nuclear position trait      
APO:0000119 size of nucleus trait      
APO:0000120 actin cytoskeleton morphology trait      
APO:0000144 telomere length trait      
APO:0000197 colony sectoring trait      
APO:0000200 budding pattern trait      
APO:0000212 bud morphology trait      
APO:0000213 spindle morphology trait      
APO:0000214 position of spindle pole body trait      
APO:0000223 mating projection morphology trait      
APO:0000226 subcellular morphology trait      
APO:0000243 Golgi morphology trait      
APO:0000270 endoplasmic reticulum morphology trait      
APO:0000273 nucleolar morphology trait      
APO:0000335 size of nucleolus trait      
APO:0000025 axial budding pattern trait      
APO:0000026 bipolar budding pattern trait      
APO:0000044 sporulation efficiency trait      
APO:0000111 viability trait      
APO:0000336 aneuploidy trait      
APO:0000337 polyploidy trait      
APO:0000048 virulence trait      
APO:0000216 fitness trait      
APO:0000218 redox state trait      
APO:0000297 mitochondrial distribution trait      
APO:0000298 peroxisomal distribution trait      
APO:0000299 vacuolar distribution trait      
APO:0000300 endoplasmic reticulum distribution trait      
APO:0000301 Golgi distribution trait      
APO:0000302 vesicle distribution trait      
APO:0000327 hydrostatic pressure resistance trait      
APO:0000034 mating efficiency trait      
APO:0000104 mitochondrial rho mutation frequency trait      
APO:0000110 competitive fitness trait      
APO:0000147 heat sensitivity trait      
APO:0000148 cold sensitivity trait      
APO:0000154 petite-negative trait      
APO:0000194 ionizing radiation resistance trait      
APO:0000195 gamma ray resistance trait      
APO:0000198 mutation frequency trait      
APO:0000315 plasma membrane morphology trait      
APO:0000326 desiccation resistance trait      
APO:0000241 freeze-thaw resistance trait      
APO:0000242 lipid particle morphology trait      
APO:0000303 endomembrane system morphology trait      
APO:0000316 chronological lifespan trait      
APO:0000317 replicative lifespan trait      
APO:0000307 anaerobic growth trait      
APO:0000308 fermentative growth trait      
APO:0000309 respiratory growth trait      
APO:0000095 chemical compound accumulation trait      
APO:0000109 survival rate in stationary phase trait      
APO:0000141 critical cell size at START (G1 cellsize checkpoint) trait      
APO:0000209 protein/peptide distribution trait      
APO:0000215 toxin resistance trait      
APO:0000030 lifespan trait      
APO:0000149 protein/peptide accumulation trait      
APO:0000224 RNA accumulation trait      
APO:0000274 prion state trait      
APO:0000201 acid pH resistance trait      
APO:0000202 alkaline pH resistance trait      
APO:0000203 hypoosmotic stress resistance trait      
APO:0000204 hyperosmotic stress resistance trait      
APO:0000205 ionic stress resistance trait      
APO:0000080 stress resistance trait      
APO:0000081 killer toxin resistance trait      
APO:0000082 osmotic stress resistance trait      
APO:0000083 oxidative stress resistance trait      
APO:0000084 radiation resistance trait      
APO:0000085 UV resistance trait      
APO:0000086 X ray resistance trait      
APO:0000032 resistance to chemicals trait      
APO:0000090 metal resistance trait      
APO:0000091 starvation resistance trait      
APO:0000092 temperature sensitive growth trait      
APO:0000093 thermotolerance trait      
APO:0000333 acquired thermotolerance trait      
APO:0000334 innate thermotolerance trait      
APO:0000199 chitin deposition trait      
APO:0000106 vegetative growth trait      
APO:0000310 growth in exponential phase trait      
APO:0000102 respiratory metabolism   GO:0045333 cellular respiration  
APO:0000101 fermentative metabolism   GO:0006113 fermentation broad
APO:0000022 protein activity   GO:0003824 catalytic activity narrow
APO:0000024 budding   GO:0007114 cell budding  
APO:0000027 filamentous growth   GO:0030447 filamentous growth  
APO:0000028 invasive growth   GO:0036267 invasive filamentous growth  
APO:0000029 pseudohyphal growth   GO:0007124 pseudohyphal growth  
APO:0000032 mating response   GO:0019236 response to pheromone broad
APO:0000033 cell fusion   GO:0140253 cell-cell fusion  
APO:0000035 nuclear fusion during mating   GO:0048288 nuclear membrane fusion involved in karyogamy  
APO:0000036 pheromone production   GO:0042811 pheromone biosynthetic process  
APO:0000037 pheromone sensitivity   GO:0019236 response to pheromone broad
APO:0000038 shmoo formation   GO:0031382 mating projection formation  
APO:0000039 meiosis   GO:0051321 meiotic cell cycle  
APO:0000040 meiotic recombination   GO:0007131 reciprocal meiotic recombination  
APO:0000041 sporulation   GO:0043934 sporulation  
APO:0000042 spore germination   GO:0009847 spore germination  
APO:0000043 spore wall formation   GO:0042244 spore wall assembly  
APO:0000046 silencing   GO:0031507 heterochromatin formation  
APO:0000047 transposable element transposition   GO:0006313 DNA transposition  
APO:0000065 flocculation   GO:0000128 flocculation  
APO:0000071 cytokinesis   GO:0000910 cytokinesis  
APO:0000072 mitotic cell cycle   GO:0000278 mitotic cell cycle  
APO:0000073 intracellular transport   GO:0046907 intracellular transport  
APO:0000074 autophagy   GO:0006914 autophagy  
APO:0000075 endocytosis   GO:0006897 endocytosis  
APO:0000076 mitochondrial transport   GO:0006839 mitochondrial transport  
APO:0000077 nuclear transport   GO:0051169 nuclear transport  
APO:0000078 protein secretion   GO:0009306 protein secretion  
APO:0000079 vacuolar transport   GO:0007034 vacuolar transport  
APO:0000096 nutrient utilization   GO:0031667 response to nutrient levels  
APO:0000098 utilization of carbon source   GO:0015976 carbon utilization  
APO:0000099 utilization of nitrogen source   GO:0019740 nitrogen utilization  
APO:0000100 nutrient uptake   GO:0098739 import across plasma membrane broad
APO:0000105 mitochondrial genome maintenance   GO:0000002 mitochondrial genome maintenance  
APO:0000123 recovery from pheromone-induced cell cycle arrest   GO:0000321 re-entry into mitotic cell cycle after pheromone arrest  
APO:0000124 pheromone-induced cell cycle arrest   GO:0000751 mitotic cell cycle G1 arrest in response to pheromone  
APO:0000125 utilization of phosphorus source   GO:0006794 phosphorus utilization  
APO:0000126 nuclear import   GO:0051170 import into nucleus  
APO:0000127 nuclear export   GO:0051168 nuclear export  
APO:0000128 peroxisomal transport   GO:0043574 peroxisomal transport  
APO:0000129 protein transport   GO:0006886 intracellular protein transport  
APO:0000130 small molecule transport   GO:0006810 transport broad
APO:0000131 protein/peptide modification   GO:0036211 protein modification process  
APO:0000132 RNA localization   GO:0006403 RNA localization  
APO:0000143 chromosome/plasmid maintenance   GO:0051276 chromosome organization related
APO:0000145 oxidative phosphorylation   GO:0006119 oxidative phosphorylation  
APO:0000155 apoptosis   GO:0006915 apoptotic process  
APO:0000157 utilization of iron source   GO:0031667 response to nutrient levels broad
APO:0000159 biofilm formation   GO:0042710 biofilm formation  
APO:0000196 mating type switching   GO:0007533 mating type switching  
APO:0000208 chromosome segregation   GO:0007059 chromosome segregation  
APO:0000219 utilization of sulfur source   GO:0006791 sulfur utilization  
APO:0000220 necrotic cell death   GO:0097300 programmed necrotic cell death  
APO:0000221 septum formation   GO:0000921 septin ring assembly  
APO:0000222 chemical compound excretion   GO:0007588 excretion broad
APO:0000225 mitotic recombination   GO:0006312 mitotic recombination  
APO:0000239 pexophagy   GO:0000425 pexophagy  
APO:0000240 mitophagy   GO:0000423 mitophagy  
APO:0000253 cell cycle progression   GO:0007049 cell cycle  
APO:0000254 cell cycle progression in G2 phase   GO:0000085 mitotic G2 phase  
APO:0000255 cell cycle progression in G1 phase   GO:0000080 mitotic G1 phase  
APO:0000256 cell cycle passage through START   GO:0007089 traversing start control point of mitotic cell cycle  
APO:0000257 cell cycle progression through the G2/M phase transition   GO:0000086 G2/M transition of mitotic cell cycle  
APO:0000258 cell cycle progression in M phase   GO:0000087 mitotic M phase  
APO:0000259 cell cycle passage through the metaphaseanaphase transition   GO:0007091 metaphase/anaphase transition of mitotic cell cycle  
APO:0000260 cell cycle progression in anaphase   GO:0000090 mitotic anaphase  
APO:0000262 cell cycle progression in mid anaphase   GO:0000091 mitotic anaphase A  
APO:0000263 cell cycle progression in late anaphase   GO:0000092 mitotic anaphase B  
APO:0000264 cell cycle progression in metaphase   GO:0000089 mitotic metaphase  
APO:0000265 cell cycle progression in telophase   GO:0000093 mitotic telophase  
APO:0000266 cell cycle progression in S phase   GO:0000084 mitotic S phase  
APO:0000267 entry into G0 (stationary phase)   GO:0070314 G1 to G0 transition  
APO:0000268 exit from G0 (stationary phase)   GO:0045023 G0 to G1 transition  
APO:0000269 cell cycle progression through the G1/S phase transition   GO:0044843 cell cycle G1/S phase transition  
APO:0000271 RNA modification   GO:0009451 RNA modification  
APO:0000275 prion inheritance   GO:0008150 biological_process broad
APO:0000276 prion formation   GO:0008150 biological_process broad
APO:0000277 prion loss   GO:0008150 biological_process broad
APO:0000288 adhesion   GO:0007155 cell adhesion  
APO:0000312 cell death   GO:0008219 cell death  
APO:0000338 micronucleophagy   GO:0044804 nucleophagy broad
APO:0000339 ribophagy   GO:0034517 ribophagy  
APO:0000340 reticulophagy   GO:0061709 reticulophagy  
APO:0000341 nucleophagy   GO:0044804 nucleophagy  
APO:0000342 late nucleophagy   GO:0044804 nucleophagy broad

@ValWood
Copy link

ValWood commented Feb 21, 2024 •
edited
Loading

This separation between traits and processes is very useful for GO too @pgaudet. This distinction between organization and morphology crops up a lot. There are other terms described as traits which sit badly in GO (i.e related to telomere length and mitochondrial ditribution.

Some minor suggestions.

APO:0000046 silencing -> GO:0031507heterochromatin formation
Silencing is broader than heterochromatin formation because Transcriptional gene silencing is the combination of heterochromatin formation and decay via surveillance
See for eg
https://pubmed.ncbi.nlm.nih.gov/33574613/
https://pubmed.ncbi.nlm.nih.gov/33723424/
summarized nicely:
Screenshot 2024-02-21 at 08 21 21
Silencing requires the coordinated action of both the RNA surveillance and the heterochromatin machinery (I hope that we can get a more precise term to represent TGS in GO- to be discussed)

APO:0000096 nutrient utilization GO:0031667 response to nutrient levels
Response to nutrient levels is broader (this aligns with how you describe ‘utilisation of iron source)

APO:0000221 septum formation GO:0000921 septin ring assembly
GO:0000917 division septum assembly
Is probably the correct term here as the septin ring and the septum are independent? (Maybe septic ring assembly in GO should move under GO:0000917 ?)
ignore this one, obs budding yeast doesn't build a division septum!

APO:0000253 cell cycle progression GO:0007049 cell cycle (in the current GO organisation this is broad because it includes cell cycle events in addition to "control of progression", (although I would like this to change eventually).

For these, note that they should probably be related, because these terms describe 'phases' not processes (they should really be in a different ontology), and they don't describe progression. We have used these in FYPO logical defs but the qualifiers are always related to progression (i.e delay, duration etc)
APO:0000254 cell cycle progression in G2 phase GO:0000085 mitotic G2 phase
APO:0000255 cell cycle progression in G1 phase GO:0000080 mitotic G1 phase
APO:0000258 cell cycle progression in M phase GO:0000087 mitotic M phase
APO:0000260 cell cycle progression in anaphase GO:0000090 mitotic anaphase
APO:0000262 cell cycle progression in mid anaphase GO:0000091 mitotic anaphase A
APO:0000263 cell cycle progression in late anaphase GO:0000092 mitotic anaphase B
APO:0000264 cell cycle progression in metaphase GO:0000089 mitotic metaphase
APO:0000265 cell cycle progression in telophase GO:0000093 mitotic telophase
APO:0000266 cell cycle progression in S phase GO:0000084 mitotic S phase

This was referenced Feb 21, 2024
Closed
Open
@matentzn
Copy link
Collaborator Author

@srengel @ValWood fantastic job, this will help us get started!
@rays22 can you can you turn @srengel work in conjunction with @ValWood comment into a google sheet in SSSOM format please, make it world-readable and share it here again?

@matentzn
Copy link
Collaborator Author

matentzn commented Mar 14, 2024 •
edited by rays22
Loading

I have created this spreadsheet for APO because I need to progress fast:

https://docs.google.com/spreadsheets/d/1pQ4VBAtfFOHLEdr1V5-4PtrtQsK50mLMQKhJ8GRpDjY/edit#gid=0

@rays22 I have not curated anything yet in there, just FYI that you dont create a new source of truth when you get to it.

  • I have not factored in @ValWood suggestions so that needs to be done as a priority

@rays22 rays22 moved this from Todo Next to In Progress in @rays22's triage and progress Mar 15, 2024
@rays22 rays22 mentioned this issue Mar 20, 2024
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@rays22 rays22

Labels
None yet
Projects
@rays22's triage and progress
Status: In Progress
Milestone
No milestone
Development

No branches or pull requests
4 participants
@matentzn @ValWood @srengel @rays22