Moving inferred classification to imports

[dosumis]

Move all inferred classification to an imported file and switch to flush and replace for inference. Editors will be able to check the results of edits by running existing reports.

Tasks:

• Review & clean up classifications marked: EXISTS, TAGGED-INFERRED, NOT-ENTAILED (ETINE)
  • [x] Make tsv for review: etines.tsv. Columns: class_id, class_name, superclass_id, superclass_name, status (1/0), manual (1/0), Entailed - checked in protege (1/0), Redundant (1/0), Fixed (1/0), Notes (free text)
  • [x] Review - following strategy doc

[cmungall]

Did we decide on how to handle this in the context of OE import behavior? I think this should be possible if we annotate the subclass axioms in the imported file, but we need to test this. Or we could just have a post-processing step where we remove these.

[dosumis]

We should be able to use a filtered save with a link filter - in addition to the term filter on ID we currently use to save only GO terms:

[cmungall]

[Edited to consolidate & clarify AIs. DOS]

Prior to switching the inference pipeline:

• [x] Using information in etines.tsv, strip 'inferred-from=true tag where status = 1 and manual =1. This needs to be scripted.

Changes to inference pipeline:

• [x] Move (tagged) inferred classifications to an imported file https://github.com/ontodev/robot/issues/66 https://github.com/ontodev/robot/pull/81
• [x] Ensure classifications are tagged https://github.com/ontodev/robot/issues/67 https://github.com/ontodev/robot/pull/81
• [x] switch off assertion in TG (or TBD: change TG architecture) @hdietze
  • (Better to generate the assertions, but push the imported file?)
  • Treat relaxation to relationship differently to actual inference? Should these actually be in the editor's file? They don't come in via other routes anymore?
• [ ] create a new report: https://github.com/geneontology/go-site/issues/195
• [ ] sign off from all editors that they have updated their OE config
  • [x] @dosumis
  • [ ] @mcourtot
  • [ ] @paolaroncaglia
  • [x] @tberardini
  • [ ] @ukemi
• [x] modify jenkins job build.berkeleybop.org/view/GO/job/build-go-assert-inferences
  • Runs with every commit, and regenerates go_inferences.obo
• [x] ensure redundant axioms are only removed from release files, never editors: https://github.com/ontodev/robot/issues/16
  • Note - It should be possible to devise a safe redundancy stripping mechanism for the editors file once we can easily separate instantiated inferences.
• [ ] Add more documentation about how editing practises will change = OE setup @dosumis

https://github.com/ontodev/robot/issues/67

[cmungall]

EDITED (if you got an email from the previous change, ignore)

This is the diff when we strip the S=1 M=1 etines (note that for provenance we retain is_manual=true).

[Term]
id: GO:0000237 ! leptotene
-is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase
+is_a: GO:0098764 {is_manual="true"} ! meiosis I cell cycle phase

[Term]
id: GO:0000238 ! zygotene
-is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase
+is_a: GO:0098764 {is_manual="true"} ! meiosis I cell cycle phase

[Term]
id: GO:0000239 ! pachytene
-is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase
+is_a: GO:0098764 {is_manual="true"} ! meiosis I cell cycle phase

[Term]
id: GO:0000240 ! diplotene
-is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase
+is_a: GO:0098764 {is_manual="true"} ! meiosis I cell cycle phase

[Term]
id: GO:0000241 ! diakinesis
-is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase
+is_a: GO:0098764 {is_manual="true"} ! meiosis I cell cycle phase

[Term]
id: GO:0000758 ! agglutination involved in conjugation with mutual genetic exchange
-is_a: GO:0000771 {is_inferred="true"} ! agglutination involved in conjugation
+is_a: GO:0000771 {is_manual="true"} ! agglutination involved in conjugation

[Term]
id: GO:0000914 ! phragmoplast assembly
-is_a: GO:1902407 {is_inferred="true"} ! assembly of actomyosin apparatus involved in mitotic cytokinesis
+is_a: GO:1902407 {is_manual="true"} ! assembly of actomyosin apparatus involved in mitotic cytokinesis

[Term]
id: GO:0006286 ! base-excision repair, base-free sugar-phosphate removal
-is_a: GO:0098502 {is_inferred="true"} ! DNA dephosphorylation
+is_a: GO:0098502 {is_manual="true"} ! DNA dephosphorylation

[Term]
id: GO:0006853 ! carnitine shuttle
-is_a: GO:1990542 {is_inferred="true"} ! mitochondrial transmembrane transport
+is_a: GO:1990542 {is_manual="true"} ! mitochondrial transmembrane transport

[Term]
id: GO:0007042 ! lysosomal lumen acidification
-is_a: GO:0007035 {is_inferred="true"} ! vacuolar acidification
+is_a: GO:0007035 {is_manual="true"} ! vacuolar acidification

[Term]
id: GO:0007128 ! meiotic prophase I
-is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase
+is_a: GO:0098764 {is_manual="true"} ! meiosis I cell cycle phase

[Term]
id: GO:0007132 ! meiotic metaphase I
-is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase
+is_a: GO:0098764 {is_manual="true"} ! meiosis I cell cycle phase

[Term]
id: GO:0007134 ! meiotic telophase I
-is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase
+is_a: GO:0098764 {is_manual="true"} ! meiosis I cell cycle phase

[Term]
id: GO:0008320 ! protein transmembrane transporter activity
-is_a: GO:0022884 {is_inferred="true"} ! macromolecule transmembrane transporter activity
+is_a: GO:0022884 {is_manual="true"} ! macromolecule transmembrane transporter activity

[Term]
id: GO:0008979 ! prophage integrase activity
-is_a: GO:0008907 {is_inferred="true"} ! integrase activity
+is_a: GO:0008907 {is_manual="true"} ! integrase activity

[Term]
id: GO:0015557 ! arginine targeting transmembrane transporter activity
-is_a: GO:0008320 {is_inferred="true"} ! protein transmembrane transporter activity
+is_a: GO:0008320 {is_manual="true"} ! protein transmembrane transporter activity

[Term]
id: GO:0019538 ! protein metabolic process
-is_a: GO:0043170 {is_inferred="true"} ! macromolecule metabolic process
+is_a: GO:0043170 {is_manual="true"} ! macromolecule metabolic process

[Term]
id: GO:0021784 ! postganglionic parasympathetic fiber development
-is_a: GO:0048483 {is_inferred="true"} ! autonomic nervous system development
+is_a: GO:0048483 {is_manual="true"} ! autonomic nervous system development

[Term]
id: GO:0030163 ! protein catabolic process
-is_a: GO:0009057 {is_inferred="true"} ! macromolecule catabolic process
+is_a: GO:0009057 {is_manual="true"} ! macromolecule catabolic process

[Term]
id: GO:0042740 ! exogenous antibiotic catabolic process
-is_a: GO:0017001 {is_inferred="true"} ! antibiotic catabolic process
+is_a: GO:0017001 {is_manual="true"} ! antibiotic catabolic process

[Term]
id: GO:0043690 ! cell-cell adhesion involved in flocculation via cell wall protein-carbohydrate interaction
-is_a: GO:0043689 {is_inferred="true"} ! cell-cell adhesion involved in flocculation
+is_a: GO:0043689 {is_manual="true"} ! cell-cell adhesion involved in flocculation

[Term]
id: GO:0043707 ! cell adhesion involved in single-species biofilm formation in or on host organism
-is_a: GO:0043709 {is_inferred="true"} ! cell adhesion involved in single-species biofilm formation
+is_a: GO:0043709 {is_manual="true"} ! cell adhesion involved in single-species biofilm formation

[Term]
id: GO:0044844 ! meiotic interphase II
-is_a: GO:0051328 {is_inferred="true"} ! meiotic interphase
-is_a: GO:0098765 {is_inferred="true"} ! meiosis II cell cycle phase
+is_a: GO:0051328 {is_manual="true"} ! meiotic interphase
+is_a: GO:0098765 {is_manual="true"} ! meiosis II cell cycle phase

[Term]
id: GO:0045476 ! nurse cell apoptotic process
-is_a: GO:0003006 {is_inferred="true"} ! developmental process involved in reproduction
+is_a: GO:0003006 {is_manual="true"} ! developmental process involved in reproduction

[Term]
id: GO:0050892 ! intestinal absorption
-is_a: GO:0022600 {is_inferred="true"} ! digestive system process
+is_a: GO:0022600 {is_manual="true"} ! digestive system process

[Term]
id: GO:0060136 ! embryonic process involved in female pregnancy
-is_a: GO:0048609 {is_inferred="true"} ! multicellular organismal reproductive process
+is_a: GO:0048609 {is_manual="true"} ! multicellular organismal reproductive process

[Term]
id: GO:0060530 ! smooth muscle cell differentiation involved in prostate glandular acinus development
-is_a: GO:0003006 {is_inferred="true"} ! developmental process involved in reproduction
+is_a: GO:0003006 {is_manual="true"} ! developmental process involved in reproduction

[Term]
id: GO:0060706 ! cell differentiation involved in embryonic placenta development
-is_a: GO:0003006 {is_inferred="true"} ! developmental process involved in reproduction
+is_a: GO:0003006 {is_manual="true"} ! developmental process involved in reproduction

[Term]
id: GO:0060742 ! epithelial cell differentiation involved in prostate gland development
-is_a: GO:0003006 {is_inferred="true"} ! developmental process involved in reproduction
+is_a: GO:0003006 {is_manual="true"} ! developmental process involved in reproduction

[Term]
id: GO:0061009 ! common bile duct development
-is_a: GO:0035295 {is_inferred="true"} ! tube development
+is_a: GO:0035295 {is_manual="true"} ! tube development

[Term]
id: GO:0061691 ! detoxification of hydrogen peroxide
-is_a: GO:0042743 {is_inferred="true"} ! hydrogen peroxide metabolic process
+is_a: GO:0042743 {is_manual="true"} ! hydrogen peroxide metabolic process

[Term]
id: GO:0071050 ! snoRNA polyadenylation
-is_a: GO:0031126 {is_inferred="true"} ! snoRNA 3'-end processing
+is_a: GO:0031126 {is_manual="true"} ! snoRNA 3'-end processing

[Term]
id: GO:0072520 ! seminiferous tubule development
-is_a: GO:0035295 {is_inferred="true"} ! tube development
+is_a: GO:0035295 {is_manual="true"} ! tube development

[Term]
id: GO:0080162 ! intracellular auxin transport
-is_a: GO:0060919 {is_inferred="true"} ! auxin influx
+is_a: GO:0060919 {is_manual="true"} ! auxin influx

[Term]
id: GO:0098765 ! meiosis II cell cycle phase
-is_a: GO:0098762 {is_inferred="true"} ! meiotic cell cycle phase
+is_a: GO:0098762 {is_manual="true"} ! meiotic cell cycle phase

[Term]
id: GO:0098768 ! meiotic prometaphase I
-is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase
+is_a: GO:0098764 {is_manual="true"} ! meiosis I cell cycle phase

[Term]
id: GO:1901487 ! negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolic process in response to increased oxygen levels
-is_a: GO:1901486 {is_inferred="true"} ! negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolic process
+is_a: GO:1901486 {is_manual="true"} ! negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolic process

[Term]
id: GO:1901619 ! tRNA methylation in response to nitrogen starvation
-is_a: GO:0030488 {is_inferred="true"} ! tRNA methylation
+is_a: GO:0030488 {is_manual="true"} ! tRNA methylation

[Term]
id: GO:1902178 ! fibroblast growth factor receptor apoptotic signaling pathway
-is_a: GO:0008543 {is_inferred="true"} ! fibroblast growth factor receptor signaling pathway
+is_a: GO:0008543 {is_manual="true"} ! fibroblast growth factor receptor signaling pathway

[Term]
id: GO:1903445 ! protein transport from ciliary membrane to plasma membrane
-is_a: GO:0015031 {is_inferred="true"} ! protein transport
-is_a: GO:0090002 {is_inferred="true"} ! establishment of protein localization to plasma membrane
+is_a: GO:0015031 {is_manual="true"} ! protein transport
+is_a: GO:0090002 {is_manual="true"} ! establishment of protein localization to plasma membrane

[cmungall]

TG now no longer asserts inferences.

As a test I added this:

[Term]
id: GO:1905270
name: Meynert cell differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires the specialized features of a Meynert cell." [GO_REF:0000086, GOC:TermGenie, PMID:4142639]
intersection_of: GO:0030154 ! cell differentiation
intersection_of: results_in_acquisition_of_features_of CL:2000056 ! Meynert cell
created_by: cjm
creation_date: 2016-06-15T23:44:17Z

As expected, this is in GO without any is_as. In the inferred file we expect this to be intermediate between two existing classes

As expected, Jenkins redballs due to apparent isa-incompleteness. The pipeline is now changed so this is allowed in editors.

[cmungall]

Everyone should also confirm they see this in P5:

• [x] @dosumis
• [ ] @mcourtot
• [ ] @paolaroncaglia
• [ ] @tberardini
• [ ] @ukemi

[dosumis]

I just realised the file on the repo is out of date, did you commit changes to the trunk? 5' job to update. Sorry!!!

On 16 Jun 2016, at 00:45, Chris Mungall notifications@github.com wrote:

This is the diff when we remove the S=1 M=1 etines:

[Term] id: GO:0000237 ! leptotene -is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase

[Term] id: GO:0000238 ! zygotene -is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase

[Term] id: GO:0000239 ! pachytene -is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase

[Term] id: GO:0000240 ! diplotene -is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase

[Term] id: GO:0000241 ! diakinesis -is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase

[Term] id: GO:0000758 ! agglutination involved in conjugation with mutual genetic exchange -is_a: GO:0000771 {is_inferred="true"} ! agglutination involved in conjugation

[Term] id: GO:0000914 ! phragmoplast assembly -is_a: GO:1902407 {is_inferred="true"} ! assembly of actomyosin apparatus involved in mitotic cytokinesis

[Term] id: GO:0006286 ! base-excision repair, base-free sugar-phosphate removal -is_a: GO:0098502 {is_inferred="true"} ! DNA dephosphorylation

[Term] id: GO:0006853 ! carnitine shuttle -is_a: GO:1990542 {is_inferred="true"} ! mitochondrial transmembrane transport

[Term] id: GO:0007042 ! lysosomal lumen acidification -is_a: GO:0007035 {is_inferred="true"} ! vacuolar acidification

[Term] id: GO:0007128 ! meiotic prophase I -is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase

[Term] id: GO:0007132 ! meiotic metaphase I -is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase

[Term] id: GO:0007134 ! meiotic telophase I -is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase

[Term] id: GO:0008320 ! protein transmembrane transporter activity -is_a: GO:0022884 {is_inferred="true"} ! macromolecule transmembrane transporter activity

[Term] id: GO:0008979 ! prophage integrase activity -is_a: GO:0008907 {is_inferred="true"} ! integrase activity

[Term] id: GO:0015557 ! arginine targeting transmembrane transporter activity -is_a: GO:0008320 {is_inferred="true"} ! protein transmembrane transporter activity

[Term] id: GO:0019538 ! protein metabolic process -is_a: GO:0043170 {is_inferred="true"} ! macromolecule metabolic process

[Term] id: GO:0021784 ! postganglionic parasympathetic fiber development -is_a: GO:0048483 {is_inferred="true"} ! autonomic nervous system development

[Term] id: GO:0030163 ! protein catabolic process -is_a: GO:0009057 {is_inferred="true"} ! macromolecule catabolic process

[Term] id: GO:0042740 ! exogenous antibiotic catabolic process -is_a: GO:0017001 {is_inferred="true"} ! antibiotic catabolic process

[Term] id: GO:0043690 ! cell-cell adhesion involved in flocculation via cell wall protein-carbohydrate interaction -is_a: GO:0043689 {is_inferred="true"} ! cell-cell adhesion involved in flocculation

[Term] id: GO:0043707 ! cell adhesion involved in single-species biofilm formation in or on host organism -is_a: GO:0043709 {is_inferred="true"} ! cell adhesion involved in single-species biofilm formation

[Term] id: GO:0044844 ! meiotic interphase II -is_a: GO:0051328 {is_inferred="true"} ! meiotic interphase -is_a: GO:0098765 {is_inferred="true"} ! meiosis II cell cycle phase

[Term] id: GO:0045476 ! nurse cell apoptotic process -is_a: GO:0003006 {is_inferred="true"} ! developmental process involved in reproduction

[Term] id: GO:0050892 ! intestinal absorption -is_a: GO:0022600 {is_inferred="true"} ! digestive system process

[Term] id: GO:0060136 ! embryonic process involved in female pregnancy -is_a: GO:0048609 {is_inferred="true"} ! multicellular organismal reproductive process

[Term] id: GO:0060530 ! smooth muscle cell differentiation involved in prostate glandular acinus development -is_a: GO:0003006 {is_inferred="true"} ! developmental process involved in reproduction

[Term] id: GO:0060706 ! cell differentiation involved in embryonic placenta development -is_a: GO:0003006 {is_inferred="true"} ! developmental process involved in reproduction

[Term] id: GO:0060742 ! epithelial cell differentiation involved in prostate gland development -is_a: GO:0003006 {is_inferred="true"} ! developmental process involved in reproduction

[Term] id: GO:0061009 ! common bile duct development -is_a: GO:0035295 {is_inferred="true"} ! tube development

[Term] id: GO:0061691 ! detoxification of hydrogen peroxide -is_a: GO:0042743 {is_inferred="true"} ! hydrogen peroxide metabolic process

[Term] id: GO:0071050 ! snoRNA polyadenylation -is_a: GO:0031126 {is_inferred="true"} ! snoRNA 3'-end processing

[Term] id: GO:0072520 ! seminiferous tubule development -is_a: GO:0035295 {is_inferred="true"} ! tube development

[Term] id: GO:0080162 ! intracellular auxin transport -is_a: GO:0060919 {is_inferred="true"} ! auxin influx

[Term] id: GO:0098765 ! meiosis II cell cycle phase -is_a: GO:0098762 {is_inferred="true"} ! meiotic cell cycle phase

[Term] id: GO:0098768 ! meiotic prometaphase I -is_a: GO:0098764 {is_inferred="true"} ! meiosis I cell cycle phase

[Term] id: GO:1901487 ! negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolic process in response to increased oxygen levels -is_a: GO:1901486 {is_inferred="true"} ! negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolic process

[Term] id: GO:1901619 ! tRNA methylation in response to nitrogen starvation -is_a: GO:0030488 {is_inferred="true"} ! tRNA methylation

[Term] id: GO:1902178 ! fibroblast growth factor receptor apoptotic signaling pathway -is_a: GO:0008543 {is_inferred="true"} ! fibroblast growth factor receptor signaling pathway

[Term] id: GO:1903445 ! protein transport from ciliary membrane to plasma membrane -is_a: GO:0015031 {is_inferred="true"} ! protein transport -is_a: GO:0090002 {is_inferred="true"} ! establishment of protein localization to plasma membrane — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[paolaroncaglia]

Mentioning @rebeccafoulger too as she also does some editing.

[tberardini]

Trying to view in Protege (admittedly, I'm still on v. 4.3) but using the same URL as in your screenshot, I ended up loading purl.obolibrary.org/obo/go/releases/2016-06-15/go.owl, and do not get the same view

. Am I not seeing the equivalence axioms and inferred parentage because of the Protege 4.3 version or because the go.owl version didn't have the data?

[cmungall]

@tberardini that's expected behavior for the public PURL

But as an editor you would have the repo checked out and open gene_ontology_write.obo directly in Protege

Of course you can't open obo in p4, so everyone should erase p4 from their hard drives :-)