search

obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
Creative Commons Zero v1.0 Universal
76 stars 17 forks source link

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

Open matentzn opened 5 months ago

matentzn commented 5 months ago

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
rays22 commented 5 months ago

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

srengel commented 4 months ago

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 commented 4 months ago

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.

1. 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)

2. 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)

3. ~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!

4. 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).

5. 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

matentzn commented 4 months ago

@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 commented 3 months ago

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.