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Progress on Annotation extension relations Progress on Annotation extension relations

Progress on Annotation extension relations - PowerPoint Presentation

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Progress on Annotation extension relations - PPT Presentation

GO editors agreed on C16 relations QuickGO graph of relations much less flat 32 51 Progress on Annotation extension relations David OS transferred all C16 relations Wiki pages to GitHub and created new pages ID: 574167

github occurs annotation annotations occurs github annotations annotation relations dependent process regulates examples relation presence terms geneontology page rachael

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Slide1

Progress on Annotation extension relations

GO editors agreed on C16 relations QuickGO graph of relations much less flat

32

51Slide2

Progress on Annotation extension relations

David OS transferred all C16 relations Wiki pages to

GitHub and created new pagesRachael and Ruth checked all GitHub pages

Edited where formatting errors existedRaised tickets for RO file edits requiredIdentified pages without usage examplesDavid OS edited RO files and reloaded to GitHubSlide3

Example GitHub

pagehttps://github.com/geneontology/annotation_extensions/blob/master/doc/

has_direct_input.mdSlide4

Example

GitHub

page

https://github.com/geneontology/annotation_extensions/blob/master/doc/

has_direct_input.mdSlide5

Use of relations slated for deprecation

David OS created file of AE annotations

Each annotation row unrolled to give a single AE relation per line (to enable sorting)Rachael and Ruth looked at use of dependent_on and in_presence_of

(over 4000 annotations) and extracted examples of use/misuseRama organised AE annotation calls (Rama, Petra, Ruth, Rachael provided examples)for majority of cases alternative ways of capturing were agreedIn some cases it was agreed that the example was outside range of GOhttp://wiki.geneontology.org/index.php/Annotation_Conf._Call,_July_28,

_2015 http://wiki.geneontology.org/index.php/Annotation_Conf._Call,_August_11,

_2015

Slide6

Consistent use of relations

86,600 AE annotationsRuth, Rachael, Rama reviewed relation use in all annotations

Status of term

No relations

No. annotations

Mostly

c

orrect

use

20+

>55000

Slated for

deprecation

7

~5116

edits

required*

~21

?

not yet in use (

May 2015)15

*Difficult to assess all but some are obvious from just looking:

e.g. 113 MF/BPs part_of (CL or

Uberon

) should

be

occurs_in

Slide7

Edits required

...some are obvious from just lookingSlide8

Deprecated terms?

Around 5000 annotations (~6% of extended annotations)Revise where possible?What about annotations outside of scope?

Continue to display?

dependent_on

in_absence_of

?

independent_of

in_presence_of

?

localization_dependent_on

requires_substance

✔requires_sequence_feature

agreed previously

?

still to be decidedSlide9

Completion of GitHub

page examples 6

1 relationships

# relationship

GitHub

page

Usage example

Folding example

13 *

-

-

-

25

-

-

23

Some

of the ‘completed’ examples need further

discussion

*

Causally_upstream_of

no

GitHub

page, is this controversial?Slide10

Relations still to be discussed/resolved

dependent_on – decided to deprecate at last callpart_of (GO ID) –

use with GO IDs to be revisedin_absence_of in_presence_of regulates_o_occurs_in

– confusing usage, see laterPetra’s example to be modeled in NoctuaSlide11

Discussions from calls

Exists_during

-> rename to ‘during’ to avoid confusion?

Requires_substance

-> we should not be recording cofactors, these should be in the definition

of the GO term

-> can use

activated_by

for activators (needs to be allowed for AE)

Independent_of

-> term is deprecated, but can we capture this type of concept in other ways?

-> we should not make negative terms, e.g.

parkin

-independent

mitophagy

Many annotations using controversial relations, e.g.

dependent_on

could be

expressed using a different relation or GO termSlide12

Discussions from calls cont’d

In_presence_of

/

dependent_on

-> we should avoid recording experimental assay details

-> if cofactor, this should be in GO term definition

->

GitHub

https://github.com/geneontology/annotation_extensions/issues/

17

In_absence_of

(to be discussed further)

annotations:

nucleus

in_absence_of

cAMP

cytosol in_presence_of cAMP PMID:24653039“We report here that GtaC exhibits rapid nucleocytoplasmic shuttling in response to periodic cAMP waves.” p1329Slide13

label: regulates process that occurs inLocal domain: GO:0050789 : regulation of biological

processDefinition: A relation that holds between a regulatory process and the entity which the regulated biological process or molecular function occurs in.Usage:

Use this relation to link a regulatory process or function to the structure that the regulated process or function occurs in.Currently no examples available on

GitHub pageWould expect this to just relate to BPs that involve whole cell processesRegulation of apoptosisRegulation of action potentialRegulation of mitotic cell cycleSome groups using ‘occurs_in’ rather than regulates_o_occurs_in

Regulation of transcriptionRegulation of signaling

regulates_o_occurs_inSlide14

If you are describing the regulatory process, then you should use theconventional relations (e.g.

occurs_in)If you are describing the GO process or function that is the target of theregulation, then you should use the chain relation

(e.g. regulates_o_occurs_in)'

regulation of transcription, DNA dependent' occurs_in 'fibroblast'means that the regulatory process occurs in a fibroblast‘regulation of transcription, DNA dependent' regulates_o_occurs_in 'fibroblast' means that the 'transcription, DNA dependent' occurs in a

fibroblast

regulates_o_occurs_in

cont’d

MGI guidelinesSlide15

Re-annotation?

Terms slated for deprecation

>5000 annotationsInconsistently used terms? annotations

Annotations to deprecated terms (e.g. during, not_exists_during)only 50 left!