OAK associations command
This notebook is intended as a supplement to the main OAK CLI docs.
This notebook provides examples for the associations command which ways of querying associations.
For more on associations, see Associations and Curated Annotations in the OAK guide.
For more on command line usage in general, see the Command Line Tutorial
Help Option
You can get help on any OAK command using --help
[1]:
!runoak associations --help
Usage: runoak associations [OPTIONS] [TERMS]...
Lookup associations from or to entities.
Example:
runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations
The above will show all associations
To query using an ontology term, including is-a closure, specify one or more
terms or term queries, plus the closure predicate(s), e.g.
Example:
runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations -p i
HP:0001392
This shows all annotations either to "Abnormality of the liver"
(HP:0001392), or to is-a descendants.
Using input specifications:
It can be awkward to specify both input ontology and association path and
format. You can use input specifications to bundle common combinations of
inputs together.
For example, the go-dictybase-input-spec combines go plus dictybase
associations.
Example:
runoak --i src/oaklib/conf/go-dictybase-input-spec.yaml associations -p
i,p GO:0008104
More examples:
https://github.com/INCATools/ontology-access-
kit/blob/main/notebooks/Commands/Associations.ipynb
Options:
-o, --output FILENAME Output file, e.g. obo file
-p, --predicates TEXT A comma-separated list of predicates. This
may be a shorthand (i, p) or CURIE
--autolabel / --no-autolabel If set, results will automatically have
labels assigned [default: autolabel]
-O, --output-type TEXT Desired output type
-o, --output FILENAME Output file, e.g. obo file
--if-absent [absent-only|present-only]
determines behavior when the value is not
present or is empty.
-S, --set-value TEXT the value to set for all terms for the given
property.
--association-predicates TEXT A comma-separated list of predicates for the
association relation
-Q, --terms-role [subject|object|both]
How to interpret query terms. [default:
object]
--help Show this message and exit.
Set up an alias
We will set up an alias for running OAK bound to GO for the purposes of this notebook:
[2]:
alias go runoak -i sqlite:obo:go
[3]:
go ontology-metadata --all
id:
- obo:go/extensions/go-plus.owl
dce:description:
- The Gene Ontology (GO) provides a framework and set of concepts for describing the
functions of gene products from all organisms.
dce:title:
- Gene Ontology
dcterms:license:
- <http://creativecommons.org/licenses/by/4.0/>
oio:default-namespace:
- gene_ontology
oio:hasOBOFormatVersion:
- '1.2'
owl:versionIRI:
- obo:go/releases/2023-04-01/extensions/go-plus.owl
owl:versionInfo:
- '2023-04-01'
rdf:type:
- owl:Ontology
sh:prefix:
- obo
schema:url:
- http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
rdfs:isDefinedBy:
- http://purl.obolibrary.org/obo/obo.owl
Check that queries work
[4]:
go info "kinase activity"
GO:0016301 ! kinase activity
Query for associations to a gene
Here we will query from a previously downloaded GAF all associations to a gene
[8]:
go -g input/gene_association.sgd.gaf -G gaf associations -Q subject SGD:S000004294 -O csv | head -20
subject predicate object object_label property_values subject_label predicate_label negated publications primary_knowledge_source aggregator_knowledge_source
SGD:S000004294 None GO:0003824 None MET17 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000004294 None GO:0003824 None MET17 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000004294 None GO:0003824 None MET17 None None SGD_REF:S000148669 infores:UniProt None
SGD:S000004294 None GO:0005737 None MET17 None None SGD_REF:S000148669 infores:UniProt None
SGD:S000004294 None GO:0005737 None MET17 None None SGD_REF:S000148671 infores:UniProt None
SGD:S000004294 None GO:0005737 None MET17 None None SGD_REF:S000069459|PMID:11914276 infores:SGD None
SGD:S000004294 None GO:0005737 None MET17 None None SGD_REF:S000069459|PMID:11914276 infores:SGD None
SGD:S000004294 None GO:0016765 None MET17 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000004294 None GO:0030170 None MET17 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000004294 None GO:0030170 None MET17 None None SGD_REF:S000185201 infores:GO_Central None
SGD:S000004294 None GO:0006520 None MET17 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000004294 None GO:0008152 None MET17 None None SGD_REF:S000148669 infores:UniProt None
SGD:S000004294 None GO:0008652 None MET17 None None SGD_REF:S000148669 infores:UniProt None
SGD:S000004294 None GO:0009086 None MET17 None None SGD_REF:S000148669 infores:UniProt None
SGD:S000004294 None GO:0019344 None MET17 None None SGD_REF:S000148669 infores:UniProt None
SGD:S000004294 None GO:0019344 None MET17 None None SGD_REF:S000075748|PMID:15042590 infores:SGD None
SGD:S000004294 None GO:0071266 None MET17 None None SGD_REF:S000204515 infores:GOC None
SGD:S000004294 None GO:0003961 None MET17 None None SGD_REF:S000124037 infores:UniProt None
SGD:S000004294 None GO:0003961 None MET17 None None SGD_REF:S000057063|PMID:3299001 infores:SGD None
Query for associations to a term
In contrast to gene queries, we want to make use of ontology relationships - in particular we typically want to include all is-a and part-of descendants in our query
[9]:
go -g input/gene_association.sgd.gaf -G gaf associations -p i,p "kinase activity" -O csv | head -20
subject predicate object object_label property_values subject_label predicate_label negated publications primary_knowledge_source aggregator_knowledge_source
SGD:S000001369 None GO:0016301 None PFK26 None None SGD_REF:S000148669 infores:UniProt None
SGD:S000001369 None GO:0003873 None PFK26 None None SGD_REF:S000124037 infores:UniProt None
SGD:S000001369 None GO:0003873 None PFK26 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000001369 None GO:0003873 None PFK26 None None SGD_REF:S000051318|PMID:1322693 infores:SGD None
SGD:S000001369 None GO:0003873 None PFK26 None None SGD_REF:S000048479|PMID:1657152 infores:SGD None
SGD:S000002318 None GO:0004708 None STE7 None None SGD_REF:S000041791|PMID:8668180 infores:SGD None
SGD:S000002318 None GO:0004708 None STE7 None None SGD_REF:S000045748|PMID:8384702 infores:SGD None
SGD:S000003272 None GO:0004707 None KSS1 None None SGD_REF:S000041791|PMID:8668180 infores:SGD None
SGD:S000003272 None GO:0004707 None KSS1 None None SGD_REF:S000045641|PMID:8918885 infores:SGD None
SGD:S000003272 None GO:0004707 None KSS1 None None SGD_REF:S000124037 infores:UniProt None
SGD:S000003272 None GO:0004707 None KSS1 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000006124 None GO:0004672 None TPK2 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000006124 None GO:0004672 None TPK2 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000006124 None GO:0004672 None TPK2 None None SGD_REF:S000113918|PMID:16319894 infores:SGD None
SGD:S000006124 None GO:0004672 None TPK2 None None SGD_REF:S000113918|PMID:16319894 infores:SGD None
SGD:S000002318 None GO:0016301 None STE7 None None SGD_REF:S000148669 infores:UniProt None
SGD:S000000364 None GO:0004674 None CDC28 None None SGD_REF:S000086178|PMID:16096060 infores:SGD None
SGD:S000000364 None GO:0004674 None CDC28 None None SGD_REF:S000146417|PMID:21841787 infores:SGD None
SGD:S000000364 None GO:0004674 None CDC28 None None SGD_REF:S000149310|PMID:22521784 infores:SGD None
SGD:S000003820 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000002394 None None GO:0009927 histidine phosphotransfer kinase activity []
SGD:S000001644 None None GO:0004693 cyclin-dependent protein serine/threonine kinase activity []
SGD:S000004710 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000001949 None None GO:0008865 fructokinase activity []
SGD:S000003607 None None GO:0003991 acetylglutamate kinase activity []
SGD:S000001075 None None GO:0004349 glutamate 5-kinase activity []
SGD:S000002924 None None GO:0019158 mannokinase activity []
SGD:S000003509 None None GO:0004140 dephospho-CoA kinase activity []
SGD:S000004438 None None GO:0008865 fructokinase activity []
SGD:S000001651 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000001681 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000002427 None None GO:0004849 uridine kinase activity []
SGD:S000003866 None None GO:0019200 carbohydrate kinase activity []
SGD:S000000687 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000006071 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000004438 None None GO:0004340 glucokinase activity []
SGD:S000001654 None None GO:0009931 calcium-dependent protein serine/threonine kinase activity []
SGD:S000001949 None None GO:0004340 glucokinase activity []
SGD:S000005878 None None GO:0004683 calmodulin-dependent protein kinase activity []
SGD:S000006074 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000003126 None None GO:0004683 calmodulin-dependent protein kinase activity []
SGD:S000001622 None None GO:0008353 RNA polymerase II CTD heptapeptide repeat kinase activity []
SGD:S000005488 None None GO:0004693 cyclin-dependent protein serine/threonine kinase activity []
SGD:S000002924 None None GO:0008865 fructokinase activity []
SGD:S000003222 None None GO:0008865 fructokinase activity []
SGD:S000002266 None None GO:0004693 cyclin-dependent protein serine/threonine kinase activity []
SGD:S000006043 None None GO:0008353 RNA polymerase II CTD heptapeptide repeat kinase activity []
SGD:S000004438 None None GO:0019158 mannokinase activity []
SGD:S000000545 None None GO:0019158 mannokinase activity []
SGD:S000002656 None None GO:0046316 gluconokinase activity []
SGD:S000002924 None None GO:0004340 glucokinase activity []
SGD:S000001654 None None GO:0004683 calmodulin-dependent protein kinase activity []
SGD:S000003222 None None GO:0019158 mannokinase activity []
SGD:S000000632 None None GO:0019200 carbohydrate kinase activity []
SGD:S000001141 None None GO:0016301 kinase activity []
SGD:S000002915 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000005776 None None GO:0051731 polynucleotide 5'-hydroxyl-kinase activity []
SGD:S000000601 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000003222 None None GO:0004340 glucokinase activity []
SGD:S000000612 None None GO:0019200 carbohydrate kinase activity []
SGD:S000006130 None None GO:0035174 histone serine kinase activity []
SGD:S000003701 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000003437 None None GO:0004849 uridine kinase activity []
SGD:S000003818 None None GO:0004550 nucleoside diphosphate kinase activity []
SGD:S000002516 None None GO:0019150 D-ribulokinase activity []
SGD:S000002691 None None GO:0004672 protein kinase activity []
SGD:S000001124 None None GO:0004672 protein kinase activity []
SGD:S000004965 None None GO:0004672 protein kinase activity []
SGD:S000003631 None None GO:0004672 protein kinase activity []
SGD:S000001297 None None GO:0004672 protein kinase activity []
SGD:S000005242 None None GO:0004672 protein kinase activity []
SGD:S000001910 None None GO:0004672 protein kinase activity []
SGD:S000005376 None None GO:0004672 protein kinase activity []
SGD:S000003324 None None GO:0004672 protein kinase activity []
SGD:S000001531 None None GO:0004672 protein kinase activity []
SGD:S000000015 None None GO:0004672 protein kinase activity []
SGD:S000006125 None None GO:0004672 protein kinase activity []
SGD:S000003593 None None GO:0004672 protein kinase activity []
SGD:S000001121 None None GO:0004672 protein kinase activity []
SGD:S000004086 None None GO:0004672 protein kinase activity []
SGD:S000002266 None None GO:0004672 protein kinase activity []
SGD:S000003942 None None GO:0004672 protein kinase activity []
SGD:S000003272 None None GO:0004672 protein kinase activity []
SGD:S000005251 None None GO:0004672 protein kinase activity []
SGD:S000002186 None None GO:0004672 protein kinase activity []
SGD:S000000931 None None GO:0004672 protein kinase activity []
SGD:S000003664 None None GO:0004672 protein kinase activity []
SGD:S000005952 None None GO:0004672 protein kinase activity []
SGD:S000001357 None None GO:0004672 protein kinase activity []
SGD:S000001599 None None GO:0004672 protein kinase activity []
SGD:S000002373 None None GO:0004672 protein kinase activity []
SGD:S000006074 None None GO:0004672 protein kinase activity []
SGD:S000004747 None None GO:0004672 protein kinase activity []
SGD:S000005947 None None GO:0004672 protein kinase activity []
SGD:S000001072 None None GO:0004672 protein kinase activity []
SGD:S000002885 None None GO:0004672 protein kinase activity []
SGD:S000005963 None None GO:0004672 protein kinase activity []
SGD:S000004354 None None GO:0004672 protein kinase activity []
SGD:S000000999 None None GO:0004672 protein kinase activity []
SGD:S000003723 None None GO:0004672 protein kinase activity []
SGD:S000003700 None None GO:0004672 protein kinase activity []
SGD:S000001649 None None GO:0004672 protein kinase activity []
SGD:S000002655 None None GO:0004672 protein kinase activity []
SGD:S000001177 None None GO:0004672 protein kinase activity []
SGD:S000005098 None None GO:0004672 protein kinase activity []
SGD:S000000925 None None GO:0004672 protein kinase activity []
SGD:S000005488 None None GO:0004672 protein kinase activity []
SGD:S000000364 None None GO:0016301 kinase activity []
SGD:S000000036 None None GO:0016301 kinase activity []
SGD:S000003818 None None GO:0016301 kinase activity []
SGD:S000000605 None None GO:0016301 kinase activity []
SGD:S000000224 None None GO:0016301 kinase activity []
SGD:S000001949 None None GO:0016301 kinase activity []
SGD:S000003222 None None GO:0016301 kinase activity []
SGD:S000001649 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000001649 None None GO:0016301 kinase activity []
SGD:S000002175 None None GO:0016301 kinase activity []
SGD:S000003700 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000002266 None None GO:0016301 kinase activity []
SGD:S000002175 None None GO:0004672 protein kinase activity []
SGD:S000006124 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000002266 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000006124 None None GO:0016301 kinase activity []
SGD:S000002318 None None GO:0004672 protein kinase activity []
SGD:S000002318 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000002634 None None GO:0016301 kinase activity []
SGD:S000002634 None None GO:0019205 nucleobase-containing compound kinase activity []
SGD:S000002580 None None GO:0016301 kinase activity []
SGD:S000004821 None None GO:0016301 kinase activity []
SGD:S000003664 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000003664 None None GO:0004713 protein tyrosine kinase activity []
SGD:S000002931 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000002931 None None GO:0016301 kinase activity []
SGD:S000003623 None None GO:0016301 kinase activity []
SGD:S000000854 None None GO:0016301 kinase activity []
SGD:S000001248 None None GO:0004672 protein kinase activity []
SGD:S000001248 None None GO:0016301 kinase activity []
SGD:S000001609 None None GO:0004672 protein kinase activity []
SGD:S000001609 None None GO:0016301 kinase activity []
SGD:S000004086 None None GO:0016301 kinase activity []
SGD:S000003272 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000002691 None None GO:0016301 kinase activity []
SGD:S000001507 None None GO:0016301 kinase activity []
SGD:S000001507 None None GO:0019205 nucleobase-containing compound kinase activity []
SGD:S000002862 None None GO:0016301 kinase activity []
SGD:S000001297 None None GO:0016301 kinase activity []
SGD:S000000112 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000000112 None None GO:0016301 kinase activity []
SGD:S000005952 None None GO:0016301 kinase activity []
SGD:S000000545 None None GO:0004396 hexokinase activity []
SGD:S000000545 None None GO:0016301 kinase activity []
SGD:S000005587 None None GO:0004672 protein kinase activity []
SGD:S000004615 None None GO:0016301 kinase activity []
SGD:S000004123 None None GO:0016301 kinase activity []
SGD:S000003810 None None GO:0016301 kinase activity []
SGD:S000005251 None None GO:0016301 kinase activity []
SGD:S000000071 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000005127 None None GO:0004672 protein kinase activity []
SGD:S000005127 None None GO:0016301 kinase activity []
SGD:S000003324 None None GO:0016301 kinase activity []
SGD:S000006074 None None GO:0004713 protein tyrosine kinase activity []
SGD:S000006074 None None GO:0016301 kinase activity []
SGD:S000000301 None None GO:0004672 protein kinase activity []
SGD:S000000301 None None GO:0016301 kinase activity []
SGD:S000005376 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000005376 None None GO:0016301 kinase activity []
SGD:S000004230 None None GO:0016301 kinase activity []
SGD:S000001177 None None GO:0016301 kinase activity []
SGD:S000005098 None None GO:0016301 kinase activity []
SGD:S000004833 None None GO:0016301 kinase activity []
SGD:S000000601 None None GO:0016301 kinase activity []
SGD:S000000687 None None GO:0016301 kinase activity []
SGD:S000000529 None None GO:0016301 kinase activity []
SGD:S000000669 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000000669 None None GO:0016301 kinase activity []
SGD:S000003087 None None GO:0016301 kinase activity []
SGD:S000001599 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000001599 None None GO:0016301 kinase activity []
SGD:S000006125 None None GO:0016301 kinase activity []
SGD:S000000015 None None GO:0016301 kinase activity []
SGD:S000003942 None None GO:0004712 protein serine/threonine/tyrosine kinase activity []
SGD:S000003942 None None GO:0016301 kinase activity []
SGD:S000004603 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000004603 None None GO:0016301 kinase activity []
SGD:S000001686 None None GO:0004430 1-phosphatidylinositol 4-kinase activity []
SGD:S000001686 None None GO:0016301 kinase activity []
SGD:S000000767 None None GO:0016301 kinase activity []
SGD:S000000105 None None GO:0016301 kinase activity []
SGD:S000001664 None None GO:0016301 kinase activity []
SGD:S000003723 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000003723 None None GO:0016301 kinase activity []
SGD:S000001915 None None GO:0016301 kinase activity []
SGD:S000001915 None None GO:0016307 phosphatidylinositol phosphate kinase activity []
SGD:S000003827 None None GO:0016301 kinase activity []
SGD:S000001681 None None GO:0016301 kinase activity []
SGD:S000001654 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000001654 None None GO:0016301 kinase activity []
SGD:S000001651 None None GO:0004672 protein kinase activity []
SGD:S000001651 None None GO:0016301 kinase activity []
SGD:S000001644 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000001644 None None GO:0004672 protein kinase activity []
SGD:S000001644 None None GO:0016301 kinase activity []
SGD:S000001550 None None GO:0016301 kinase activity []
SGD:S000001508 None None GO:0004672 protein kinase activity []
SGD:S000004296 None None GO:0016301 kinase activity []
SGD:S000000164 None None GO:0016301 kinase activity []
SGD:S000000184 None None GO:0016301 kinase activity []
SGD:S000000340 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000000340 None None GO:0016301 kinase activity []
SGD:S000004747 None None GO:0016301 kinase activity []
SGD:S000001003 None None GO:0016301 kinase activity []
SGD:S000001075 None None GO:0016301 kinase activity []
SGD:S000001124 None None GO:0016301 kinase activity []
SGD:S000003701 None None GO:0016301 kinase activity []
SGD:S000000931 None None GO:0016301 kinase activity []
SGD:S000006130 None None GO:0016301 kinase activity []
SGD:S000002616 None None GO:0016301 kinase activity []
SGD:S000002616 None None GO:0016307 phosphatidylinositol phosphate kinase activity []
SGD:S000006130 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000002259 None None GO:0016301 kinase activity []
SGD:S000005963 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000005211 None None GO:0016301 kinase activity []
SGD:S000001409 None None GO:0000155 phosphorelay sensor kinase activity []
SGD:S000001409 None None GO:0016301 kinase activity []
SGD:S000000925 None None GO:0016301 kinase activity []
SGD:S000001357 None None GO:0016301 kinase activity []
SGD:S000001304 None None GO:0016301 kinase activity []
SGD:S000003420 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000006258 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000006258 None None GO:0004672 protein kinase activity []
SGD:S000006258 None None GO:0016301 kinase activity []
SGD:S000006135 None None GO:0016301 kinase activity []
SGD:S000003437 None None GO:0016301 kinase activity []
SGD:S000003636 None None GO:0016301 kinase activity []
SGD:S000001861 None None GO:0016301 kinase activity []
SGD:S000003593 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000003593 None None GO:0016301 kinase activity []
SGD:S000003820 None None GO:0016301 kinase activity []
SGD:S000003866 None None GO:0016301 kinase activity []
SGD:S000002237 None None GO:0004672 protein kinase activity []
SGD:S000002237 None None GO:0016301 kinase activity []
SGD:S000003051 None None GO:0004672 protein kinase activity []
SGD:S000003027 None None GO:0016301 kinase activity []
SGD:S000003494 None None GO:0016301 kinase activity []
SGD:S000005310 None None GO:0016301 kinase activity []
SGD:S000005330 None None GO:0016301 kinase activity []
SGD:S000005200 None None GO:0016301 kinase activity []
SGD:S000005105 None None GO:0004672 protein kinase activity []
SGD:S000005105 None None GO:0016301 kinase activity []
SGD:S000004965 None None GO:0016301 kinase activity []
SGD:S000004535 None None GO:0016301 kinase activity []
SGD:S000004535 None None GO:0050354 triokinase activity []
SGD:S000001072 None None GO:0016301 kinase activity []
SGD:S000000871 None None GO:0016301 kinase activity []
SGD:S000003631 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000003631 None None GO:0004713 protein tyrosine kinase activity []
SGD:S000002898 None None GO:0016301 kinase activity []
SGD:S000000999 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000000999 None None GO:0016301 kinase activity []
SGD:S000002604 None None GO:0016301 kinase activity []
SGD:S000001622 None None GO:0016301 kinase activity []
SGD:S000002924 None None GO:0004396 hexokinase activity []
SGD:S000002924 None None GO:0016301 kinase activity []
SGD:S000002516 None None GO:0016301 kinase activity []
SGD:S000004250 None None GO:0008481 sphinganine kinase activity []
SGD:S000004250 None None GO:0003951 NAD+ kinase activity []
SGD:S000004438 None None GO:0004396 hexokinase activity []
SGD:S000004438 None None GO:0016301 kinase activity []
SGD:S000006109 None None GO:0003951 NAD+ kinase activity []
SGD:S000003958 None None GO:0016301 kinase activity []
SGD:S000006179 None None GO:0016301 kinase activity []
SGD:S000006157 None None GO:0004672 protein kinase activity []
SGD:S000006157 None None GO:0016301 kinase activity []
SGD:S000002325 None None GO:0016301 kinase activity []
SGD:S000002427 None None GO:0016301 kinase activity []
SGD:S000002183 None None GO:0016301 kinase activity []
SGD:S000006071 None None GO:0016301 kinase activity []
SGD:S000005645 None None GO:0016301 kinase activity []
SGD:S000005645 None None GO:0004674 protein serine/threonine kinase activity []
SGD:S000005488 None None GO:0016301 kinase activity []
SGD:S000005460 None None GO:0016301 kinase activity []
SGD:S000005697 None None GO:0016301 kinase activity []
SGD:S000005697 None None GO:0008481 sphinganine kinase activity []
SGD:S000002915 None None GO:0016301 kinase activity []
SGD:S000005422 None None GO:0016301 kinase activity []
SGD:S000005473 None None GO:0016301 kinase activity []
SGD:S000005496 None None GO:0016301 kinase activity []
SGD:S000005947 None None GO:0016301 kinase activity []
SGD:S000002885 None None GO:0016301 kinase activity []
Note that including part of (p) does not make a difference with the MF hierarchy in GO, but does make a big difference in the other two.
Important: closures make a big difference
Let’s compare the number of results with and without closures
[10]:
go -g input/gene_association.sgd.gaf -G gaf associations -p i,p "kinase activity" -O csv | wc
3209 32091 315394
[11]:
go -g input/gene_association.sgd.gaf -G gaf associations "kinase activity" -O csv | wc
285 2851 26750
Complex Queries
We can use the OAK graph query language to specify exhaustive lists of direct terms.
For example, not retrieve annotations to any kinase that is not a protein kinase:
[12]:
go -g input/gene_association.sgd.gaf -G gaf associations .desc//p=i "kinase activity" .not .desc//p=i "protein kinase activity" -O csv | head -30
subject predicate object object_label property_values subject_label predicate_label negated publications primary_knowledge_source aggregator_knowledge_source
SGD:S000001369 None GO:0016301 None PFK26 None None SGD_REF:S000148669 infores:UniProt None
SGD:S000001369 None GO:0003873 None PFK26 None None SGD_REF:S000124037 infores:UniProt None
SGD:S000001369 None GO:0003873 None PFK26 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000001369 None GO:0003873 None PFK26 None None SGD_REF:S000051318|PMID:1322693 infores:SGD None
SGD:S000001369 None GO:0003873 None PFK26 None None SGD_REF:S000048479|PMID:1657152 infores:SGD None
SGD:S000002318 None GO:0016301 None STE7 None None SGD_REF:S000148669 infores:UniProt None
SGD:S000000605 None GO:0004618 None PGK1 None None SGD_REF:S000058483|PMID:6254992 infores:SGD None
SGD:S000000605 None GO:0004618 None PGK1 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000000605 None GO:0004618 None PGK1 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000000605 None GO:0004618 None PGK1 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000000605 None GO:0004618 None PGK1 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000000605 None GO:0004618 None PGK1 None None SGD_REF:S000124037 infores:UniProt None
SGD:S000003818 None GO:0004798 None CDC8 None None SGD_REF:S000053290|PMID:6088527 infores:SGD None
SGD:S000003818 None GO:0004798 None CDC8 None None SGD_REF:S000049877|PMID:6094555 infores:SGD None
SGD:S000003818 None GO:0004798 None CDC8 None None SGD_REF:S000130762|PMID:19540237 infores:SGD None
SGD:S000003818 None GO:0004798 None CDC8 None None SGD_REF:S000130762|PMID:19540237 infores:SGD None
SGD:S000003818 None GO:0004798 None CDC8 None None SGD_REF:S000053290|PMID:6088527 infores:SGD None
SGD:S000003818 None GO:0004798 None CDC8 None None SGD_REF:S000042433|PMID:6091111 infores:SGD None
SGD:S000003818 None GO:0004798 None CDC8 None None SGD_REF:S000042433|PMID:6091111 infores:SGD None
SGD:S000003818 None GO:0004798 None CDC8 None None SGD_REF:S000124037 infores:UniProt None
SGD:S000003818 None GO:0004798 None CDC8 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000003818 None GO:0004798 None CDC8 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000003818 None GO:0009041 None CDC8 None None SGD_REF:S000049877|PMID:6094555 infores:SGD None
SGD:S000002939 None GO:0004594 None CAB1 None None SGD_REF:S000124037 infores:UniProt None
SGD:S000002939 None GO:0004594 None CAB1 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000002939 None GO:0004594 None CAB1 None None SGD_REF:S000129524|PMID:19266201 infores:SGD None
SGD:S000002939 None GO:0004594 None CAB1 None None SGD_REF:S000065722|PMID:9890959 infores:SGD None
SGD:S000002939 None GO:0004594 None CAB1 None None SGD_REF:S000124037 infores:UniProt None
SGD:S000002939 None GO:0004594 None CAB1 None None SGD_REF:S000124036 infores:InterPro None
SGD:S000001357 None None GO:0016301 kinase activity []
SGD:S000001304 None None GO:0016301 kinase activity []
SGD:S000006258 None None GO:0016301 kinase activity []
SGD:S000006135 None None GO:0016301 kinase activity []
SGD:S000003437 None None GO:0016301 kinase activity []
SGD:S000003636 None None GO:0016301 kinase activity []
SGD:S000001861 None None GO:0016301 kinase activity []
SGD:S000003593 None None GO:0016301 kinase activity []
SGD:S000003820 None None GO:0016301 kinase activity []
SGD:S000003866 None None GO:0016301 kinase activity []
SGD:S000002237 None None GO:0016301 kinase activity []
SGD:S000003027 None None GO:0016301 kinase activity []
SGD:S000003494 None None GO:0016301 kinase activity []
SGD:S000005310 None None GO:0016301 kinase activity []
SGD:S000005330 None None GO:0016301 kinase activity []
SGD:S000005200 None None GO:0016301 kinase activity []
SGD:S000005105 None None GO:0016301 kinase activity []
SGD:S000004965 None None GO:0016301 kinase activity []
SGD:S000004535 None None GO:0016301 kinase activity []
SGD:S000004535 None None GO:0050354 triokinase activity []
SGD:S000001072 None None GO:0016301 kinase activity []
SGD:S000000871 None None GO:0016301 kinase activity []
SGD:S000002898 None None GO:0016301 kinase activity []
SGD:S000000999 None None GO:0016301 kinase activity []
SGD:S000002604 None None GO:0016301 kinase activity []
SGD:S000001622 None None GO:0016301 kinase activity []
SGD:S000002924 None None GO:0004396 hexokinase activity []
SGD:S000002924 None None GO:0016301 kinase activity []
SGD:S000002516 None None GO:0016301 kinase activity []
SGD:S000004250 None None GO:0008481 sphinganine kinase activity []
SGD:S000004250 None None GO:0003951 NAD+ kinase activity []
SGD:S000004438 None None GO:0004396 hexokinase activity []
SGD:S000004438 None None GO:0016301 kinase activity []
SGD:S000006109 None None GO:0003951 NAD+ kinase activity []
SGD:S000003958 None None GO:0016301 kinase activity []
SGD:S000006179 None None GO:0016301 kinase activity []
SGD:S000006157 None None GO:0016301 kinase activity []
SGD:S000002325 None None GO:0016301 kinase activity []
SGD:S000002427 None None GO:0016301 kinase activity []
SGD:S000002183 None None GO:0016301 kinase activity []
SGD:S000006071 None None GO:0016301 kinase activity []
SGD:S000005645 None None GO:0016301 kinase activity []
SGD:S000005488 None None GO:0016301 kinase activity []
SGD:S000005460 None None GO:0016301 kinase activity []
SGD:S000005697 None None GO:0016301 kinase activity []
SGD:S000005697 None None GO:0008481 sphinganine kinase activity []
SGD:S000002915 None None GO:0016301 kinase activity []
SGD:S000005422 None None GO:0016301 kinase activity []
SGD:S000005473 None None GO:0016301 kinase activity []
SGD:S000005496 None None GO:0016301 kinase activity []
SGD:S000005947 None None GO:0016301 kinase activity []
SGD:S000002885 None None GO:0016301 kinase activity []
SGD:S000003664 None None GO:0016301 kinase activity []
SGD:S000002416 None None GO:0004335 galactokinase activity []
SGD:S000003272 None None GO:0016301 kinase activity []
SGD:S000004818 None None GO:0016301 kinase activity []
SGD:S000005878 None None GO:0016301 kinase activity []
SGD:S000003426 None None GO:0016301 kinase activity []
SGD:S000005874 None None GO:0016301 kinase activity []
SGD:S000002874 None None GO:0016301 kinase activity []
SGD:S000002554 None None GO:0016301 kinase activity []
SGD:S000002939 None None GO:0016301 kinase activity []
SGD:S000005793 None None GO:0016301 kinase activity []
SGD:S000000972 None None GO:0004017 adenylate kinase activity []
SGD:S000000972 None None GO:0016301 kinase activity []
SGD:S000000972 None None GO:0019205 nucleobase-containing compound kinase activity []
SGD:S000002644 None None GO:0016301 kinase activity []
SGD:S000002655 None None GO:0016301 kinase activity []
SGD:S000002656 None None GO:0016301 kinase activity []
Querying via API
Some association sources provide an API, so rather than downloading an association file, you have OAK speak to the API.
Note that API endpoints may not support all OAK options; e.g. the amigo endpoint currently forces you to use IDs:
[13]:
!runoak -i amigo:NCBITaxon:9606 associations -p i,p GO:0016301 | head -30
subject predicate object property_values subject_label predicate_label object_label negated publications primary_knowledge_source aggregator_knowledge_source
UniProtKB:Q13976 None GO:0004672 PRKG1 None protein kinase activity None PMID:25447536 BHF-UCL infores:go
UniProtKB:Q13976 None GO:0004692 PRKG1 None cGMP-dependent protein kinase activity None PMID:21402151 UniProt infores:go
UniProtKB:Q13976 None GO:0004692 PRKG1 None cGMP-dependent protein kinase activity None Reactome:R-HSA-418442 Reactome infores:go
UniProtKB:Q13976 None GO:0106310 PRKG1 None protein serine kinase activity None GO_REF:0000116 RHEA infores:go
UniProtKB:Q9HCP0 None GO:0004674 CSNK1G1 None protein serine/threonine kinase activity None PMID:25500533 ParkinsonsUK-UCL infores:go
UniProtKB:Q9HCP0 None GO:0106310 CSNK1G1 None protein serine kinase activity None GO_REF:0000116 RHEA infores:go
UniProtKB:Q9HCP0 None GO:0004674 CSNK1G1 None protein serine/threonine kinase activity None PMID:21873635 GO_Central infores:go
UniProtKB:Q8IWQ3 None GO:0004674 BRSK2 None protein serine/threonine kinase activity None GO_REF:0000024 ARUK-UCL infores:go
UniProtKB:Q8IWQ3 None GO:0004674 BRSK2 None protein serine/threonine kinase activity None PMID:14976552 UniProt infores:go
UniProtKB:Q8IWQ3 None GO:0050321 BRSK2 None tau-protein kinase activity None GO_REF:0000024 UniProt infores:go
UniProtKB:Q8IWQ3 None GO:0050321 BRSK2 None tau-protein kinase activity None PMID:21985311 UniProt infores:go
UniProtKB:Q8IWQ3 None GO:0050321 BRSK2 None tau-protein kinase activity None PMID:28386764 ARUK-UCL infores:go
UniProtKB:Q8IWQ3 None GO:0106310 BRSK2 None protein serine kinase activity None GO_REF:0000116 RHEA infores:go
UniProtKB:Q8IWQ3 None GO:0050321 BRSK2 None tau-protein kinase activity None PMID:21873635 GO_Central infores:go
UniProtKB:Q8IWQ3 None GO:0004674 BRSK2 None protein serine/threonine kinase activity None PMID:21873635 GO_Central infores:go
UniProtKB:Q96PF2 None GO:0004674 TSSK2 None protein serine/threonine kinase activity None GO_REF:0000024 UniProt infores:go
UniProtKB:Q96PF2 None GO:0004674 TSSK2 None protein serine/threonine kinase activity None PMID:18533145 UniProt infores:go
UniProtKB:Q96PF2 None GO:0004674 TSSK2 None protein serine/threonine kinase activity None PMID:20729278 UniProt infores:go
UniProtKB:Q96PF2 None GO:0106310 TSSK2 None protein serine kinase activity None GO_REF:0000116 RHEA infores:go
UniProtKB:Q96PF2 None GO:0004674 TSSK2 None protein serine/threonine kinase activity None PMID:21873635 GO_Central infores:go
UniProtKB:P19525 None GO:0004672 EIF2AK2 None protein kinase activity None PMID:12882984 UniProt infores:go
UniProtKB:P19525 None GO:0004672 EIF2AK2 None protein kinase activity None PMID:15229216 UniProt infores:go
UniProtKB:P19525 None GO:0004672 EIF2AK2 None protein kinase activity None PMID:18835251 UniProt infores:go
UniProtKB:P19525 None GO:0004672 EIF2AK2 None protein kinase activity None PMID:21123651 UniProt infores:go
UniProtKB:P19525 None GO:0004672 EIF2AK2 None protein kinase activity None PMID:248628414 UniProt infores:go
UniProtKB:P19525 None GO:0004674 EIF2AK2 None protein serine/threonine kinase activity None PMID:1695551 PINC infores:go
UniProtKB:P19525 None GO:0004694 EIF2AK2 None eukaryotic translation initiation factor 2alpha kinase activity None PMID:25329545 UniProt infores:go
UniProtKB:P19525 None GO:0004715 EIF2AK2 None non-membrane spanning protein tyrosine kinase activity None GO_REF:0000003 UniProt infores:go
UniProtKB:P19525 None GO:0016301 EIF2AK2 None kinase activity None PMID:21123651 UniProt infores:go
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