flybase/flybase-controlled-vocabulary

The home of the FlyBase miscellaneous ontologies - incorporating the Drosophila Phenotype Ontology (see also FlyBase/drosophila-phenotype-ontology)

Welcome to the home of the FlyBase miscellaneous ontologies

This work is licensed under a Creative Commons Attribution 4.0 International License.

The FlyBase controlled vocabulary (FBcv) incorporates a number of controlled vocabularies and ontologies developed and used by FlyBase, including the Drosophila phenotype ontology (DPO). The DPO is arguably the most important of the component ontologies and was previously maintained in this repository, but has been officially released as a separate project since 25 July 2019. The DPO can be accessed here.

Downloads:

The latest version of the ontology is available in various forms at http://purl.obolibrary.org/obo/fbcv/<filename>

Dated releases can be found at http://purl.obolibrary.org/obo/fbcv/releases/<YYYY-MM-DD>/<filename>

Descriptions of the different versions (artefacts) are available here. Files are provided in owl, obo and json format.

Base files

• fbcv-base.owl
• fbcv-base.obo
• fbcv-base.json

Full files

• fbcv-full.owl
• fbcv-full.obo
• fbcv-full.json

Non-classified files

• fbcv-non-classified.owl
• fbcv-non-classified.obo
• fbcv-non-classified.json

Simple files

• fbcv-simple.owl
• fbcv-simple.obo
• fbcv-simple.json

Publications

1. Osumi-Sutherland D., Marygold S. J., Millburn G. H., McQuilton P. A., Ponting. L., Stefancsik R., Falls K., Brown N. H., Gkoutos G. V. (2013) The Drosophila phenotype ontology. Journal of Biomedical Semantics 4(30).

Funding

Development of the FlyBase controlled vocabulary has been funded by a series of grants to FlyBase from the National Human Genome Research Institute at the U.S. National Institutes of Health.

flybase-controlled-vocabulary's Issues

Misformed PATO iri for FBcv_0006001

Theres a PATO iri that is part of the FBcv_0006001 axiom that is missing a 'h':

<owl:Class rdf:about="http://purl.obolibrary.org/obo/FBcv_0006001">
    <owl:equivalentClass>
        <owl:Class>
            <owl:intersectionOf rdf:parseType="Collection">
                <rdf:Description rdf:about="ttp://purl.obolibrary.org/obo/PATO_0001695"/>
                <owl:Restriction>
                    <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
                    <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/FBbt_00000001"/>
                </owl:Restriction>
            </owl:intersectionOf>
        </owl:Class>
 </owl:equivalentClass>

as well as part of the class definition

<!-- ttp://purl.obolibrary.org/obo/PATO_0001695 -->
   <owl:Class rdf:about="ttp://purl.obolibrary.org/obo/PATO_0001695">

Running reduce removes most of the conditionality relations

@dosumis FYI as a potential side effect of the reduce step in the simple goal..

Make sure that the robot_diff command compares with LAST PURL

Right now can be

SIMPLE_PURL = http://purl.obolibrary.org/obo/fbdv/fbdv-simple.obo

Do this for all four ontologies:

• fbdv
• fbcv
• fbbt
• dpo

PATO_0001695 wrong url format

During PATO mapping, the PATO_0001695 IRI was somehow broken. If you check fbcv.owl, and search for

ttp://purl.obolibrary.org/obo/PATO_0001695

you can see that for some reason, the "h" in the beginning of the URL is missing. This can cause problems with mapping this ontology to others in the long run.

'binding tool' terms

New terms to use with experimental tools that specifically bind to something, to go under 'experimental tool descriptor' branch of FBcv

A. summary of tree:

   specific binding tool
       purification tag
       antibody
	      nanobody
       epitope tag
       conditional specific binding tool
	      light-regulated specific binding tool
	      small molecule-regulated specific binding tool
	      temperature-regulated specific binding tool

B. New CV terms requested:

[Term]
id: FBcv:NEW
name: specific binding tool
namespace: experimental_tool_descriptor
def: "Sequence that has a property that allows specific binding to another macromolecule." [FBC:GM]
is_a: FBcv:0005001 ! experimental tool descriptor

[Term]
id: FBcv:NEW
name: conditional specific binding tool
namespace: experimental_tool_descriptor
def: "Sequence that has a property that allows specific binding to another macromolecule, where this property can be regulated in response to a particular stimulus." [FBC:GM]
is_a: FBcv:NEW ! specific binding tool

[Term]
id: FBcv:NEW
name: light-regulated specific binding tool
namespace: experimental_tool_descriptor
def: "Sequence that has a property that allows specific binding to another macromolecule, where this property can be regulated by irradiation with a pulse of light." [FBC:GM]
is_a: FBcv:NEW ! specific binding tool

[Term]
id: FBcv:NEW
name: small molecule-regulated specific binding tool
namespace: experimental_tool_descriptor
def: "Sequence that has a property that allows specific binding to another macromolecule, where this property can be regulated by binding to a small molecule, such as an ion or ligand." [FBC:GM]
is_a: FBcv:NEW ! specific binding tool

[Term]
id: FBcv:NEW
name: temperature-regulated specific binding tool
namespace: experimental_tool_descriptor
def: "Sequence that has a property that allows specific binding to another macromolecule, where this property can be regulated by temperature." [FBC:GM]
is_a: FBcv:NEW ! specific binding tool

[Term]
name: antibody
namespace: experimental_tool_descriptor
def: ??see comment below??
is_a: FBcv:NEW ! specific binding tool

the experimental condition ontology term XCO:0000194 (https://www.ebi.ac.uk/ols/ontologies/xco/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FXCO_0000194) has the following definition which I think would work, but not sure the correct way to refer to this ontology term and put in the definition:

An immunoglobulin molecule having a specific amino acid sequence that gives each antibody the ability to adhere to and interact only with the antigen that induced its synthesis and with molecules containing structures similar to that antigen. An antigen is any substance capable of inducing a specific immune response, including but not limited to toxins, bacterial proteins and viruses. [ Miller-Keane:Miller-Keane_Encyclopedia_and_Dictionary_of_Medicine_Nursing_and_Allied_Health--7th_Ed ]

[Term]
name: nanobody
def: "Antigen-binding variable domain of a camelid heavy chain antibody; a single domain antibody fragment that binds a specific antigen." [FBC:GM, PMID:16095608]
is_a: FBcv:NEW ! antibody

C. edits for existing terms.

The following terms already exist in FBcv, but need an edit to place them under the new 'specific binding tool' term.

a.

id: FBcv:0005036
name: purification tag

this is currently under the tree as:

is_a: FBcv:0005001 ! experimental tool descriptor

can it be moved so that it is under 'specific binding tool' i.e. move to:

is_a: FBcv:NEW ! specific binding tool

b.

id: FBcv:0005021
name: epitope tag

this is currently listed as a child of:
is_a: FBcv:0005004 ! protein detection tool

this is fine, but can the following relationship also be added:

is_a: FBcv:NEW ! specific binding tool

Revise Flybase ontology release mechanism

FBCV used to have this system that releases were placed in parallel into the "releases" sub-directory. The question is whether we want to continue to do that, or wether we go with the "normal" way of keeping the latest version on the top level, and creating proper github releases (to which the version iris would point). I am not bothered either way. Both of them require modifications to the existing mechanisms.

Move dpo development entirely to OWL [sf#4]

Reported by djs93 on 2013-07-12 10:30 UTC
The hybrid mode of development - having some dpo terms maintained in OBO and others in OWL, is too onerous for ontology editors to maintain and makes the release pipeline far too brittle. Development of the dpo should therefore be moved entirely to OWL, with the rest staying of fbcv staying in OBO. dpo-edit.owl should import the external terms it needs from module files generated from external ontologies using oort (although we may need an extra step for FBdv module generation).

This will allow two, relatively simple release processes. One that generates dpo and another that merges dpo into fbcv to make a full fbcv release.

FBcv updates for experimental tools

Umbrella ticket for FBcv updates for experimental tools

name change for 3 '-dependent' experimental tool terms

Term name requests to change '-dependent' names to '-regulated' for experimental tool FBcv terms

This will make them consistent with other terms being introduced, plus means that if there are experimental tools where the dependency is to turn off the function of the tool in response to a change in condition (rather than turn it on), the CV term is still appropriate to use, giving greater flexibility ('-dependent' implies that the tool function is turned 'on' by the change in condition, which doesn't fit the definiton in each case, which is 'regulated').

In each case the name being changed should be retained as a synonym.

id: FBcv:0005083
name: small molecule-dependent gene product degradation tag

change name to: small molecule-regulated gene product degradation tag

id: FBcv:0005039
name: light-dependent activity regulation tag

change name to: light-regulated activity regulation tag

id: FBcv:0005040
name: small molecule-dependent activity regulation tag

change name to: small molecule-regulated activity regulation tag

Assertions about "part of" contradict BFO world view.

As I outlined in https://github.com/FlyBase/flybase-controlled-vocabulary/issues/13, I am trying to work on integrating phenotype patterns across species ontologies. DPO/FBCV makes the fundamental assertion that "part_of" is a sub-object property of "happens_during". I understand that this is part of another design pattern you are using (shortcut relations), but it would make things easier if this assertion was to be removed (it renders almost 60% of the phenotype classes unsatisfiable when the union of phenotype ontologies is considered), which makes querying across all phenotype ontologies hard. Since happens_during has a domain and range of occurrent, and many continuants use the part of relation (both are disjoint), many phenotypes are inferred to be both occurrents and continuants -> unsatifiable.

Remove dates from edit file

Remove dates from edit file (currently still needed to generate correct dates in artefacts).

Review typedefs in edit file

[Typedef]
id: conditionality
name: conditionality

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.\nThis relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
is_transitive: true
is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to

[Typedef]
id: different_in_magnitude_relative_to
name: different_in_magnitude_relative_to
def: "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]

[Typedef]
id: ends_during
name: ends_during
namespace: gene_ontology
xref: RO:0002093

[Typedef]
id: happens_during
name: happens_during
namespace: gene_ontology
xref: RO:0002092
is_transitive: true
is_a: ends_during ! ends_during

[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.\nExample: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.

[Typedef]
id: has_part
name: has_part
namespace: relationship
xref: BFO:0000051
xref: OBO_REL:has_part
is_transitive: true

[Typedef]
id: has_role
name: has role

[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.\nThis relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
is_transitive: true
is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to

[Typedef]
id: inheres_in
name: inheres_in
xref: RO:0000052

[Typedef]
id: occurs_in
name: occurs in
namespace: gene_ontology
xref: BFO:0000066
transitive_over: part_of ! part_of

[Typedef]
id: part_of
name: part_of
namespace: relationship
xref: BFO:0000050
xref: OBO_REL:part_of
is_transitive: true

[Typedef]
id: qualifier
name: qualifier
comment: temporary placeholder - this means that Obol could not infer the correct relation
subset: do_not_annotate

[Typedef]
id: reciprocal_of
name: reciprocal_of
def: "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e." [PATOC:CJM]
comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.\nThere are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.

[Typedef]
id: regulates
name: regulates
namespace: gene_ontology
xref: RO:0002211
transitive_over: part_of ! part_of

[Typedef]
id: similar_in_magnitude_relative_to
name: similar_in_magnitude_relative_to
def: "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]

[Typedef]
id: singly_occurring_form_of
name: singly_occurring_form_of
comment: PATO divides qualities between normal (monadic, singly-occurring) qualities and relational qualities. Relational qualities stand in the 'towards' relation with respect to some additional entity. For example, The sensitivity of an eye towards red light. In some cases we want to represent a quality such as 'protruding' in both monadic and relational branches. We use this relation to link them.\nPATO divides qualities between normal (monadic, singly-occurring) qualities and relational qualities. Relational qualities stand in the 'towards' relation with respect to some additional entity. For example, The sensitivity of an eye towards red light. In some cases we want to represent a quality such as 'protruding' in both monadic and relational branches. We use this relation to link them.
synonym: "monadic_form_of" EXACT []

[Typedef]
id: starts_during
name: starts_during
namespace: gene_ontology
xref: RO:0002091

[Typedef]
id: towards
name: towards
comment: temporary placeholder - may be placed in OBO_REL; with relational qualities, the additional argument is the 'towards' argument; eg sensitivity towards chlorine. Relation binding a relational quality or disposition to the relevant type of entity.

@dosumis these are the typedefs in the current fbcv-edit file. Can you check them and review which ones should be mapped to RO? I assume I can remove all annotations and axiomatisation for all Typedefs that have an RO mapping after you are done with it?

Document design patterns for behavioral phenotypes to add

Increased behavior
decreased behavior
ectopic/induced behavior

QC: add ISBN wellformed check in chado load script test

DPO and FBCV

General QC configuration for all Flybase ontologies

@Clare72

The way QC now works for all four ontologies is this:

1. We run the whole (slightly modified) pipeline (encoded in travis.sh)
2. In the end some hard QC is run. This qc can be controlled through the file called qc-profile.txt in the src/ontology directory. Open this file; it is pretty permissive now, because there are some errors. We can discuss QC levels and so on over the next months in our meetings.

Every ontology has currently slightly different QC levels; feel free to modify them as you please. If you want any custom QC, make a ticket and assign it to me, I will implement it. Once you read and understood this ticket, you can copy its contents to the editors README in fbcv src/ontology directory to keep the general documentation up to date, and close it.

neuron activity regulation tool terms

New terms to use with experimental tools that regulate neuron activity, to go under 'experimental tool descriptor' branch of FBcv

A. summary of tree:

neuron activity regulation tool

	neuron inhibition tool
		conditional neuron inhibition tool
			light-regulated neuron inhibition tool
			small molecule-regulated neuron inhibition tool
			temperature-regulated neuron inhibition tool
	neuron activation tool
		conditional neuron activation tool
			temperature-regulated neuron activation tool
			small molecule-regulated neuron activation tool
			light-regulated neuron activation tool

B. New CV terms requested:

(have put FBcv:NEW as a place-holder where one of the terms has a relationship to another of the new terms)

name: neuron activity regulation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to regulate the activity of a neuron. This is often achieved by manipulation of membrane potential or synaptic transmission dynamics." [FBC:GM]
synonym: electrically signalling cell activity regulation tool
is_a: FBcv:0005001 ! experimental tool descriptor

name: neuron inhibition tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to inhibit the activity of a neuron. This is often achieved by inducing membrane hyperpolarization (GO:0060081)." [FBC:GM]
synonym: electrically signalling cell inhibition tool
is_a: FBcv:NEW ! neuron activity regulation tool

name: conditional neuron inhibition tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to inhibit the activity of a neuron, where this property can be regulated in response to a particular stimulus." [FBC:GM]
is_a: FBcv:NEW ! neuron inhibition tool

name: light-regulated neuron inhibition tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to inhibit the activity of a neuron, where this property can be regulated by irradiation with a pulse of light." [FBC"GM]
synonym: optogenetic neuron inhibition tool
is_a: FBcv:NEW ! conditional neuron inhibition tool

name: small molecule-regulated neuron inhibition tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to inhibit the activity of a neuron, where this property can be regulated by binding to a small molecule, such as an ion or ligand." [FBC:GM]
is_a: FBcv:NEW ! conditional neuron inhibition tool

name: temperature-regulated neuron inhibition tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to inhibit the activity of a neuron, where this property can be regulated by temperature." [FBC:GM]
is_a: FBcv:NEW ! conditional neuron inhibition tool

name: neuron activation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to stimulate the activity of a neuron. This is often achieved by inducing membrane depolarization (GO:0051899)." [FBC:GM]
synonym: electrically signalling cell activation tool
is_a: FBcv:NEW ! neuron activity regulation tool

name: conditional neuron activation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to stimulate the activity of a neuron, where this property can be regulated in response to a particular stimulus." [FBC:GM]
is_a: FBcv:NEW ! neuron activation tool

name: light-regulated neuron activation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to stimulate the activity of a neuron, where this property can be regulated by irradiation with a pulse of light." [FBC"GM]
synonym: optogenetic neuron activation tool
is_a: FBcv:NEW ! conditional neuron activation tool

name: small molecule-regulated neuron activation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to stimulate the activity of a neuron, where this property can be regulated by binding to a small molecule, such as an ion or ligand." [FBC:GM]
is_a: FBcv:NEW ! conditional neuron activation tool

name: temperature-regulated neuron activation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to stimulate the activity of a neuron, where this property can be regulated by temperature." [FBC:GM]
is_a: FBcv:NEW ! conditional neuron activation tool

new genome engineering tool terms for RMCE elements

I thought it would be nice to have a pair of terms to be able to mark RMCE target and RMCE donor elements, so that researchers can easily find insertions of constructs where new drivers/fluorescent proteins etc, can easily be swapped in and out. I've made a pair of new terms for this, below.

[Term]
name: RMCE target
namespace: experimental_tool_descriptor
def: "An RMCE target element contains a region of DNA sequence flanked by a pair of target sites for a recombinase or an integrase, which are arranged such that this target sequence cassette can be replaced with donor sequence from a compatible RMCE donor element via recombination-mediated cassette exchange (RMCE). For RMCE mediated by a recombinase, the target cassette is flanked by two non-identical recombinase target sites that each carry a different mutation in the spacer sequence of the target site; this renders the two sites incompatible with each other. A compatible RMCE donor cassette is flanked by the same pair of non-identical sites; in the presence of recombinase, a double recombination event between the identical sites on the donor and target sequences results in replacement of the target cassette with the donor cassette. In the case of RMCE mediated by an integrase, the RMCE cassette is flanked by identical integrase target sites, while a compatible RMCE donor cassette is flanked by copies of the orthogonal integrase target site; in the presence of integrase, a double recombination event results in the target cassette being replaced with that of the donor cassette. In this case, if the flanking sites are in inverted orientation, replacement of the target cassette can occur in either direction." [FBC:GM, PMID:7947678, PMID:21445009, FlyBase:FBrf0231034]
is_a: FBcv:0005075 ! genome engineering tool
synonym: recombination-mediated cassette exchange target element

[Term]
name: RMCE donor
namespace: experimental_tool_descriptor
def: "An RMCE donor element contains a region of DNA sequence flanked by a pair of target sites for a recombinase or an integrase, which are arranged such that this donor sequence cassette can be used to replace target sequence of a compatible RMCE target element via recombination-mediated cassette exchange (RMCE). For RMCE mediated by a recombinase, the target cassette is flanked by two non-identical recombinase target sites that each carry a different mutation in the spacer sequence of the target site; this renders the two sites incompatible with each other. A compatible RMCE donor cassette is flanked by the same pair of non-identical sites; in the presence of recombinase, a double recombination event between the identical sites on the donor and target sequences results in replacement of the target cassette with the donor cassette. In the case of RMCE mediated by an integrase, the RMCE cassette is flanked by identical integrase target sites, while a compatible RMCE donor cassette is flanked by copies of the orthogonal integrase target site; in the presence of integrase, a double recombination event results in the target cassette being replaced with that of the donor cassette. In this case, if the flanking sites are in inverted orientation, replacement of the target cassette can occur in either direction." [FBC:GM, PMID:7947678, PMID:21445009, FlyBase:FBrf0231034]
is_a: FBcv:0005075 ! genome engineering tool
synonym: recombination-mediated cassette exchange donor element

Examples of each type:

1. RMCE target

Mi{MIC} https://flybase.org/reports/FBtp0051711
P{loxP-y-lox511} https://flybase.org/reports/FBtp0082282
PBac{806.LOX-SVS-2} https://flybase.org/reports/FBtp0065988

2. RMCE donor

P{FRT(PT-GFSTF.0)} https://flybase.org/reports/FBtp0108915
P{lox(Trojan-GAL4)x3} https://flybase.org/reports/FBtp0099339

pBS-KS-attB1-2-GT-SA-Flpo-SV40 https://flybase.org/reports/FBmc0003060
pBS-KS-attB1-2-GT-SA-GAL4-Hsp70pA https://flybase.org/reports/FBmc0003059

Questions:

• are these two terms enough, or should we perhaps also (or instead) have a more general 'swappable cassette' term, in case there are elements that have a swappable cassette that can be replaced by some other non-RMCE mechanism

• should the terms also be listed as children of insertional mutagenesis tool ?

tweak to definitions of recombinase/integrase related FBcv terms

Small change to definition of four recombinase/integrase related FBcv terms is requested to reflect community usage of RMCE to mean 'recombination-mediated cassette exchange' (which can include recombination mediated by both recombinases and integrases) rather than the more specific 'recombination-mediated cassette exchange'.

[Term]
id: FBcv:0005062
name: recombinase

please change 'recombinase-mediated cassette exchange (RMCE)' at the end of the definition to 'recombination-mediated cassette exchange (RMCE)'

[Term]
id: FBcv:0005063
name: recombinase target site

please change 'recombinase-mediated cassette exchange (RMCE)' at the end of the definition to 'recombination-mediated cassette exchange (RMCE)'

[Term]
id: FBcv:0005076
name: integrase

please change 'integrase-mediated cassette exchange (IMCE)' at the end of the definition to 'recombination-mediated cassette exchange (RMCE)'

[Term]
id: FBcv:0005079
name: integrase target site

please change 'integrase-mediated cassette exchange (IMCE)' at the end of the definition to 'recombination-mediated cassette exchange (RMCE)'

Write new code for generating autodefs for phenotype [sf#3]

Reported by djs93 on 2013-07-12 10:23 UTC

Background

In order to simplify maintenance and building of the dpo and fbcv, dpo development will be moved entirely to OWL. This will break the existing script for rolling automated definitions for phenotypes as this works by recognising particular definition patterns. This was never a great idea, given that patterns may change to take into account inference, even when the semantics of a definition do not.

Aim

Write a new script for automating definitions, based on a standard shorthand used in textual definitions.

Proposal

Ideally this would be written over the OWL-API, but given time constraints this is not going to happen. Instead it will use OBO + existing Perl modules. The major disadvantage of this is that it will require the affected definitions at least to be maintained in a separate OWL file, translated to OBO to roll autodefs, and then back again to to provide a file for generating the release.

Loss of non-redundant axiom in fbcv.obo

We are losing this relationship from FBcv:0000525 'chemical' in fbcv.obo and fbcv.owl:

is_a: FBcv:0000452 ! origin of mutation

This results in chemical terms falling under owl:Thing rather than 'origin of mutation' in the fbcv hierarchy.
This also affects fbcv-full, but not other files.

In fbcv-edit.obo:

[Term]
id: FBcv:0000525
name: chemical
namespace: origin_of_mutation
def: "$sub_CHEBI:24431" [CHEBI:24431]
synonym: "mutation induced by chemical exposure" EXACT []
is_a: FBcv:0000452 ! origin of mutation

In fbcv.obo:

[Term]
id: FBcv:0000525
name: chemical
namespace: origin_of_mutation
def: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." [CHEBI:24431]
synonym: "mutation induced by chemical exposure" EXACT []
is_a: CHEBI:24431 ! chemical entity

In both files chemical entity has:

equivalent_to: FBcv:0000525 ! chemical

non standard IDs [sf#5]

@dosumis
Reported by djs93 on 2015-05-01 23:27 UTC
A number of IDs need to be switched or mapped to an obo library standard. They were generated as scratch_{UUID}.

These include 'population of Drosophila' and the data property 'has_increased_mortality_rate'. The latter should probably be in RO (would be its first data property). 'population of Drosophila' should just get an FBcv ID. Its parent class should be mapped to PCO.

fbcv-full cannot be reduced

The full profile of FBCV involves a step where redundant axioms are stripped out. Unfortunately, much more than just redundant axioms are stripped, and I assume this is due to equivalent class cycles we need to investigate. the current workaround is the NOT do any redundancy stripping: fbcv.Makefile

# For some reason, using reduce just does not work on FBCV this is a workaround, but it needs some figuring out..

$(ONT)-full.owl: $(SRC) $(OTHER_SRC)
	$(ROBOT) merge --input $(SRC) \
		reason --reasoner ELK --equivalent-classes-allowed asserted-only \
		relax \
		annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --annotation oboInOwl:date "$(OBODATE)" --output tmp/full.owl

Modernise FBcv repo - to use starter kit, automated import generation etc

FBcv apart from dpo can remain in OBO with its own bespoke infrastructure. dpo can be moved to standard ontology starter kit with imports.

CHEBI dependency currently wrong

After the next ROBOT release, we need to change it (fbdv.Makefile) and (dpo.Makefile).

Rewrite auto_def_sub.pl in scala so that it works for all OWL files

DOS noticed this in OLS:

Make sure no "No definition" cases left

Currently, there are 32 definitions that say "No description"

[Term]
id: FBcv:0000527
name: diethyl sulfate
namespace: origin_of_mutation
def: "No description" [CHEBI:34699]
synonym: "DES" RELATED []
synonym: "mutation induced by diethyl sulfate exposure" EXACT []
is_a: FBcv:0000526 ! alkylating agent

The reason for that is that Chebi does not have definitions for quite a few terms, see for example this case here:

https://www.ebi.ac.uk/ols/ontologies/chebi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_34699

What do you want to happen in this case?

Add script for automatically generating phenotype ontology [sf#2]

Reported by djs93 on 2013-05-09 14:43 UTC
Write script to generate a set of release files with all terms in FBcv OBO namespace: phenotypic_class + any terms used in their differentia.

In an ideal world, this would be done using Oort (see this ticket for requested functionality). In the absence of this it could be done relatively straightforwardly with one of the Perl OBO libraries. But, with this strategy, this needs to be done as an this as an initial step using the fbcv-edit.obo to generate the full range of file types including complete axiomatisation. The resulting file obo can be processed as usual for release.

Verify one last time that the release is ok

Should be after all the work we put into it! :)

diff this:
https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/releases/fbcv-simple.obo
with
https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/fbcv-odk/fbcv-simple.obo

at least, maybe one last glance at the flybase release. Then you can merge the branch.

This should really be good enough by now, but let me know anything problematic.

'light conditional'

definition:

Phenotype expressed only in the presence or absence of light, which may be white light or particular wavelength(s).'

parent:

conditional (FBcv:0000309)

namespace:

environmental_qualifier

small molecule-regulated protein cleavage tag

new term request:

name: small molecule-regulated protein cleavage tag
namespace: experimental_tool_descriptor
def: "Sequence that forms part of the protein product encoded by a transgenic locus or modified endogenous locus and which allows the tagged protein product to be cleaved (broken into smaller molecules by the rupture of a covalent bond) by a specific process that can be regulated by binding to a small molecule, such as an ion or ligand." [FBC:GM]
is_a: FBcv:0005057 ! protein cleavage tag

cell ablation tool terms

New terms to use with experimental tools used to ablate cells, to go under 'experimental tool descriptor' branch of FBcv

A. summary of tree:

cell ablation tool
	conditional cell ablation tool
		temperature-regulated cell ablation tool
		light-regulated cell ablation tool
		small molecule-regulated cell ablation tool

B. New CV terms requested:

(have put FBcv:NEW as a place-holder where one of the terms has a relationship to another of the new terms)

[Term]
name: cell ablation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property used to ablate a specific cell or anatomical structure." [FBC:GM]
is_a: FBcv:0005001 ! experimental tool descriptor

[Term]
name: conditional cell ablation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property used to ablate a specific cell or anatomical structure, where this property can be regulated in response to a particular stimulus." [FBC:GM]
is_a: FBcv:NEW ! cell ablation tool

[Term]
name: temperature-regulated cell ablation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property used to ablate a specific cell or anatomical structure, where this property can be regulated by temperature." [FBC:GM]
is_a: FBcv:NEW ! conditional cell ablation tool

[Term]
name: light-regulated cell ablation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property used to ablate a specific cell or anatomical structure, where this property can be regulated by irradiation with a pulse of light." [FBC:GM]
is_a: FBcv:NEW ! conditional cell ablation tool

[Term]
name: small molecule-regulated cell ablation tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property used to ablate a specific cell or anatomical structure, where this property can be regulated by binding to a small molecule, such as an ion or ligand." [FBC:GM]
is_a: FBcv:NEW ! conditional cell ablation tool

fbcv/dpo.owl resolves to SourceForge

Related to: OBOFoundry/OBOFoundry.github.io#18

Still not 100% sure of the correct PURL to use

http://purl.obolibrary.org/obo/fbcv/dpo.owl still resolves to sourceforge - is this intended?

The ontology URI in the file is:

    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/dpo.owl">

these should match

new tool term: meganuclease

id: NEW
name: meganuclease
namespace: experimental_tool_descriptor
def: "An enzyme that catalyzes hydrolysis of DNA in a site-specific manner, having a cognate recognition site of 20-30bp. The DNA cutting stimulates cellular repair mechanisms, which can be exploited to produce genome modifications. For example, repair by homologous recombination in the presence of an exogenous template can be used to introduce targeted changes into the genome." [FB:GM, FBrf0231034]
is_a: FBcv:0005077 ! nuclease

Addition of 'micropublication' and 'preprint'

New terms to fall under 'publication class' (FBcv:0000189):

micropublication
A short report describing a single, stand-alone research finding that is peer-reviewed and published. (SJM; https://www.micropublication.org)

preprint
A version of a scientific manuscript that is shared publicly on the web without peer review. In most cases, work posted as a preprint will be submitted for peer review at a journal. (SJM; http://asapbio.org/preprint-info)

Moved from JIRA (DC-844)

docking site tool term

New term to make it easy for researchers to find all available docking site insertions

[Term]
name: docking site
namespace: experimental_tool_descriptor
def: "A docking site is an element that has been introduced into a site in the genome to allow integration of DNA at a defined location; this neutralizes the problem of position effects that are seen with non-specific insertion techniques such as transposable-element-mediated transgenesis. A docking site contains a single target site for an integrase, allowing subsequent integration of DNA into this site from a donor element via integrase mediated recombination. The docking site in the genome typically contains the 'attB' site and the donor plasmid contains the 'attP' site, since this directionality gives higher integration rates compared to the alternative combination where the 'attB' site is integrated into the genome. A docking site insertion is typically selected to be 'benign' (that is it does not result in disruption of an endogenous locus) and to show a high rate of integration in the presence of integrase." [FBC:GM, PMID:11359900, PMID:12563279, FlyBase:FBrf0194996, FlyBase:FBrf0192974]
is_a: FBcv:0005075 ! genome engineering tool
synonym: landing site

Examples

P{CaryP} https://flybase.org/reports/FBtp0018807
M{3xP3-RFP.attP} https://flybase.org/reports/FBtp0021844

Update terms imported from ChEBI

Hi !

The latest release of fbcv contains syntax errors in the terms imported from ChEBI that have since then been fixed upstream, but the changes have not been propagated to fbcv-edit.obo (e.g.

synonym: "Actinomycin" EXACT [KEGG COMPOUND:]

has changed to

synonym: "Actinomycin" EXACT [KEGG_COMPOUND]

which is correct OBO 1.4 syntax)

new experimental tool sensor terms

Term requests for tools that are used as sensors for the activity of biological processes/pathway/product, rather than just to detect the presence/absence/localization of a gene product.

NB.

• In each case I wrote 'specified' in the definition, but am not sure whether 'specific' would be better

name: biological process activity sensor
namespace: experimental_tool_descriptor
def: Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that is used to provide a readout of the activity of a specified biological process.
is_a: FBcv:0005044 | genetically encoded sensor
synonym: reporter of biological process pathway activity

example of the above for context:
https://flybase.org/reports/FBal0319233 - sensor for caspase activity (i.e. apoptosis)

name: signal transduction pathway activity sensor
namespace: experimental_tool_descriptor
def: Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that is used to provide a readout of the activity of a specified signal transduction pathway.
synonym: reporter of signal transduction pathway activity
is_a: FBcv:NEW | biological process activity sensor

name: gene product activity sensor
namespace: experimental_tool_descriptor
def: Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that is used to provide a readout of the activation state of a specified gene product.
synonym: gene product activation state detection tool
is_a: FBcv:0005044 | genetically encoded sensor

example of the above for context:
https://flybase.org/reports/FBal0243925 - biosensor for Rac activity

PURL to DPO does not resolve properly

https://purl.obolibrary.org/obo/dpo.owl
https://purl.obolibrary.org/obo/dpo

exist as per

http://obofoundry.org/ontology/dpo.html

but does not resolve. Can we redirect for example to:

https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/releases/dpo-non-classified.owl

Low importance: make project board

Maybe better to create a project board here: https://github.com/orgs/FlyBase/projects

add all four ontology repos and add all non-NTR tickets on there for now; This is not urgent, but maybe it is better to keep an overview of what needs doing in the long run.

fix typo in 'enhancer trap' definition

There is a typo in the definition of:

id: FBcv:0005069
name: enhancer trap

'mutagenic' needs changing to 'mutagenic'

split recombinase

new term request::

[Term]
name: split recombinase
namespace: experimental_tool_descriptor
def: "Catalytically inactive fragment of a recombinase. A functional recombinase can be reconstituted when complementary split recombinase fragments are brought together in vivo by fusing the fragments to peptides that physically interact." [FBC:GM]
is_a: FBcv:0005051 ! split system component

New qualifier for indicating functional/circuit phenotypes in neurons

It is currently not possible to distinguish between morphological and functional/circuit phenotypes in phenotypic class statements. Being able to do so would be useful to VFB (this was originally discussed early in the current VFB grant cycle - but seems to have never made it into a ticket).

This could potentially be achieved by add qualifiers to PC statements.

e.g. we might have the qualifier circuit phenotype for cases where manipulating that activity of one neuron changes the activity of another.

Add 'lecture' to publication class CV.

Hi Clare,

Please add this term under 'publication class' in FBcv:
Term: lecture
Def: Work consisting of speeches read or delivered before an audience or class, especially for instruction or to set forth some subject.
(taken from https://www.ncbi.nlm.nih.gov/mesh/68019531)

Add code for automating derivation of FBdv slice for lethal phase [sf#1]

@dosumis
Reported by djs93 on 2013-05-09 14:38 UTC
Spec: For life stage get EquivalentClass, Ancestors, Descendants. Get descendants for developmental stage' that part_of some 'immature adult stage'.

For now, this is generated using an OBO-Edit filtered save, but this should be replaced by an OWL-API based pipeline script.

proximity labeling tool terms

New terms for proximity labeling tools

A. summary of tree:

proximity labeling tool
	proximity labeling tool (protein)
	proximity labeling tool (RNA)
	proximity labeling tool (DNA)

B. New CV terms requested:

(have put FBcv:NEW as a place-holder where one of the terms has a relationship to another of the new terms)

[Term]
name: proximity labeling tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that encodes an enzyme which covalently tags neighbouring macromolecules, facilitating the subsequent purification or detection of the tagged macromolecules by an experimental method." [FBC:GM, PMID:30774936]
is_a: FBcv:0005001 ! experimental tool descriptor

[Term]
name: proximity labeling tool (protein)
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that encodes an enzyme which covalently tags neighbouring proteins, facilitating the subsequent purification or detection of the tagged proteins by an experimental method." [FBC:GM, PMID:29125959, PMID:30774936]
is_a: FBcv:NEW ! proximity labeling tool

[Term]
name: proximity labeling tool (RNA)
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that encodes an enzyme which covalently tags neighbouring RNA, facilitating the subsequent purification or detection of the tagged RNA by an experimental method." [FBC:GM, PMID:30774936]
is_a: FBcv:NEW ! proximity labeling tool

[Term]
name: proximity labeling tool (DNA)
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that encodes an enzyme which covalently tags neighbouring DNA, facilitating the subsequent purification or detection of the tagged DNA by an experimental method." [FBC:GM, PMID:30774936]
is_a: FBcv:NEW ! proximity labeling tool

C. Examples for context:

• proximity labeling tool (protein)

biotin ligase systems based on Ecol\birA (https://flybase.org/reports/FBgn0243509) e.g. BioID, TurboID, miniTurboID. (Need to make experimental tool reports for these different systems).

APEX https://flybase.org/reports/FBto0000405
APEX2 https://flybase.org/reports/FBto0000403

• proximity labeling tool (DNA)

DamID https://flybase.org/reports/FBto0000392

(will use new CV terms in the 'Uses' slot for the cases above where the tools already exist)

Add subset: common_tool_use to some more experimental tool terms

Please could the following subset be added to the experimental tool FBcv terms listed below (having the subset helps QA when making new transgenes of these kinds of tool):

subset: common_tool_use

to be added to:

neuron activity regulation tool (FBcv:0007002)
specific binding tool (FBcv:0007029)
proximity labeling tool (FBcv:0007021)
cell ablation tool (FBcv:0007013)

Typo in several definitions of partially lethal phenotypic class terms

Example:

some die during third instar larval stage FBcv:0002024
"A phenotype of a population that is the death a significant proportion of animals in that population during the third instar larval stage."

Similar typo in:
some die during second instar larval stage FBcv:0002022
some die during first instar larval stage FBcv:0002021
some die during larval stage FBcv:0002023
some die during pupal stage FBcv:0002039
some die during prepupal stage FBcv:0002040
some die during pharate adult stage FBcv:0002038
some die during P-stage FBcv:0002020
some die during embryonic stage FBcv:0002041
partially lethal - majority die FBcv:0000352

No name for 'inheres in part of'

Currently showing up in fbcv-simple as:

[Typedef]
id: RO:0002314
holds_over_chain: inheres_in BFO:0000050

Full typedef appears in fbcv-base.obo

tweak to definition of 'promoter trap' term

Please could the definition of the following FBcv term:

[Term]
id: FBcv:0005073
name: promoter trap
namespace: experimental_tool_descriptor

be changed from:

def: "The basic component of a promoter trap cassette is a promoterless gene. This gene is not flanked by splice acceptor or donor sites, and thus the gene within a promoter trap can only be expressed if the cassette integrates into the genome within an exon, resulting in a transcriptional fusion. If the promoter trap gene encodes an open reading frame and the insertion is in the correct frame, a translational fusion is produced. Depending on the nature of the gene encoded by the promoter trap cassette, the insertion may directly report the expression pattern of the 'trapped' locus (e.g. if the gene encoded by the cassette is a reporter enzyme or fluorescent protein), or it may be used to drive expression of any gene of interest (e.g. if the gene encoded by the cassette is a driver that form part of a binary expression system). A promoter trap cassette may be inserted into a genome as part of a transgenic construct via transposable-element-mediated transgenesis, or may be inserted directly into a modified endogenous locus via a genome engineering method such as homologous recombination or CRISPR. Promoter trap insertions are usually mutagenic, disrupting the locus into which they have inserted, since termination sequences are usually present at the 3' end of the cassette, truncating the endogenous transcript." [FBC:GM, PMID:10899970]

to

def: "The basic component of a promoter trap cassette is a promoterless gene. This gene is not flanked by splice acceptor or donor sites, and thus the gene within a promoter trap can only be expressed if the cassette integrates into the genome within an exon, resulting in a transcriptional fusion. If the promoter trap gene encodes an open reading frame (ORF) and the insertion is in the correct frame, the trap ORF may be translated from this transcriptional fusion either as a translational fusion with ORF sequence of the disrupted endogenous locus, or if an internal ribosome entry site (IRES) or viral 2A-like peptide sequence (which promotes ribosome skipping) is present upstream of the promoter trap ORF, it may be produced as a separate protein expressed under the control of the regulatory sequences of the endogenous locus. Depending on the nature of the gene encoded by the promoter trap cassette, the insertion may directly report the expression pattern of the 'trapped' locus (e.g. if the gene encoded by the cassette is a reporter enzyme or fluorescent protein), or it may be used to drive expression of any gene of interest (e.g. if the gene encoded by the cassette is a driver that form part of a binary expression system). A promoter trap cassette may be inserted into a genome as part of a transgenic construct via transposable-element-mediated transgenesis, or may be inserted directly into a modified endogenous locus via a genome engineering method such as homologous recombination or CRISPR. Promoter trap insertions are usually mutagenic, disrupting the locus into which they have inserted, since termination sequences are usually present at the 3' end of the cassette, truncating the endogenous transcript." [FBC:GM, PMID:10899970]

cell labelling tool terms

[Term]
name: cell labeling tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and that confers a specific property that can be used to facilitate the detection of a specific cell population by an experimental method." [FBC:GM]
is_a: FBcv:0005001 ! experimental tool descriptor

[Term]
name: multicolor cell labeling tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and confers a specific property that can be used to stochastically label cells in the same sample with different colors of fluorescent protein. This property can be exploited to study cell morphology and to track lineages of clonally related cells [FBC:GM, PMID:25491327]
is_a: FBcv:NEW ! cell labeling tool

(plan to use the multicolor cell labeling tool term to mark Brainbow and related constructs so that they are easy to find)