CL:Aligning species-specific anatomy ontologies with CL - Revision history

Cjm: Replacing page with 'http://obofoundry.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL'

2009-06-08T16:02:59Z

Replacing page with 'http://obofoundry.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL'

Cjm: /* Other reasoners */

2007-08-09T20:27:57Z

Other reasoners

Cjm: /* Using the reasoner */

2006-08-24T00:40:53Z

Using the reasoner

Cjm: /* Using xrefs */

2006-08-24T00:26:27Z

Using xrefs

Cjm at 00:19, 24 August 2006

2006-08-24T00:19:13Z

Cjm at 23:38, 23 August 2006

2006-08-23T23:38:44Z

New page

The OBO Cell ontology is intended to be a species-neutral reference ontology.

Species-centric anatomy ontologies may want to 'extend' CL with subtypes of cells that are specific to certain types of organism - the discussion on where the dividing line between what goes in a SCA (species-centric anatomy) ontology and CL is still open.

In addition, SCA ontology maintainers may wish to 'replicate' CL terms in their own ontology. Why? The canonical example here is:

Purkinje_cell part_of cerebellum

This assertion is universally true (all Purkinje cells are part_of some cerebellum at all times). The fact that not all organisms have a cerebellum is irrelevant. See [[RO:part_of]] for details.

Here is the problem. We have a species-neutral cell ontology with Purkinje_cell (CL:0000121), but we have no species-neutral anatomy ontology with brain parts. We do have for example the zebrafish anatomy [[ZFA:Main_Page]] which has ZFA:0000100 cerebellum. So we can say:

CL:0000121 part_of ZFA:0000100

However, this is incorrect as not all Purkinje cells are part of fish cerebellums. Whilst it is not explicitly stated whether the definition of ZFA:0000100 is scoped to any particular organism type, we get into problems if we assume the definitions apply to all organisms in which the type is instantiated, as there will be other links in ZFA that do not hold for all organisms.

If ZFA were to include a term for Purkinje cell, say ZFA:9999999, we could say:

ZFA:999999 part_of ZFA:0000100

SCA curators may have other reasons for replicating CL terms (or terms from other species-neutral reference ontologies like GO) in their ontology.

It's important that SCAs stay in sync with species neutral resources like CL and CARO [[CARO:Main_Page]]

← Older revision		Revision as of 16:02, 8 June 2009
Line 1:		Line 1:
−	~~The OBO Cell ontology is intended to be a species-neutral reference ontology.~~	+	http://obofoundry.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL
−
−	Species-centric anatomy ontologies may want to 'extend' CL with subtypes of cells that are specific to certain types of organism - the discussion on where the dividing line between what goes in a SCA (species-centric anatomy) ontology and CL is still open.
−
−	~~In addition, SCA ontology maintainers may wish to 'replicate' CL terms in their own ontology. Why? The canonical example here is:~~
−
−	~~Purkinje_cell part_of cerebellum~~
−
−	~~This assertion is universally true (all Purkinje cells are part_of some cerebellum at all times). The fact that not all organisms have a cerebellum is irrelevant. See [[RO:part_of]] for details.~~
−
−	~~Here is the problem. We have a species-neutral cell ontology with Purkinje_cell (CL:0000121), but we have no~~
−	~~species-neutral anatomy ontology with brain parts. We do have for example the zebrafish anatomy [[ZFA:Main_Page]] which has ZFA:0000100 cerebellum. So we can say:~~
−
−	~~CL:0000121 part_of ZFA:0000100~~
−
−	However, this is incorrect as not all Purkinje cells are part of fish cerebellums. Whilst it is not explicitly stated whether the definition of ZFA:0000100 is scoped to any particular organism type, we get into problems if we assume the definitions apply to all organisms in which the type is instantiated, as there will be other links in ZFA that do not hold for all organisms.
−
−	~~If ZFA were to include a term for Purkinje cell, say ZFA:9999999, we could say:~~
−
−	~~ZFA:999999 part_of ZFA:0000100~~
−
−	~~SCA curators may have other reasons for replicating CL terms (or terms from other species-neutral reference ontologies like GO) in their ontology.~~
−
−	It's important that SCAs stay in sync with species neutral resources like CL and CARO [[CARO:Main_Page]]. This can be done automatically. First the SCA editors must maintain links to the CL; then they can use a reasoner to keep the ontologies in sync.
−
−	~~=Maintaining links to CL=~~
−
−	~~The SCA editors have two options here. They can 'explicitly define' SCA specific types in terms of CL types, or they can use a more lightweight xref approach~~
−
−	~~==Explicit definitions==~~
−
−	For example, ZFA:Purkinje_cell could be defined as "A CL:Purkinje_cell 'which' is part_of a Zebrafish". This is known as a genus-differentia definition (note: genus is used in its non-linnaean sense here)
−
−	This definition must be entered via the oboedit cross-product plugin tool. (The core/generic/genus term would be "CL:Purkinje cell" and the discriminating chacteristics would be "part_of a Zebrafish"). Here is what this would look like in obo 1.2 format:
−
−	~~[Term]~~
−	~~id: ZFA:0000134~~
−	~~name: neurons~~
−	~~namespace: zebrafish_anatomy~~
−	~~xref_analog: ZFIN:ZDB-ANAT-010921-563~~
−	~~intersection_of: CL:0000540~~
−	~~intersection_of: part_of NCBITax:7955~~
−	~~relationship: end ZFS:0000044 ! Adult~~
−	~~relationship: part_of ZFA:0000396 ! nervous system~~
−	~~relationship: start ZFS:0000026 ! Segmentation:14-19 somites~~
−
−	~~You will also need a file with the appropriate taxonomic type in it - you can use the whole ncbi_taxonomy.obo file, or you can just keep a separate file with this:~~
−
−	~~[Term]~~
−	~~id: NCBITax:7955~~
−	~~name: Danio rerio~~
−
−	~~We are now ready to feed this to the reasoner~~
−
−	~~==Using xrefs==~~
−
−	The alternate, more lightweight option is to simply maintain xref links to CL. ZFA are doing this anyway (and this part could be automated via simple text-matching). These are "special" xref links in that they have additional implicit meaning. Here is an example of the underlying obo file:
−
−	~~[Term]~~
−	~~id: ZFA:0000134~~
−	~~name: neurons~~
−	~~namespace: zebrafish_anatomy~~
−	~~xref_analog: ZFIN:ZDB-ANAT-010921-563~~
−	~~xref_analog: CL:0000540~~
−	~~relationship: end ZFS:0000044 ! Adult~~
−	~~relationship: part_of ZFA:0000396 ! nervous system~~
−	~~relationship: start ZFS:0000026 ! Segmentation:14-19 somites~~
−
−	~~The only difference is the addition of an extra xref line.~~
−
−	This xref isn't enough information for the oboedit reasoner to know that the two ontologies must line up. You must convert the lightweight obo file to an obo file that contains the genus-differentia definitions. This can be done with a simple standalone script:
−
−	~~obo-promote-dbxref-to-intersection.pl --idspace CL -d part_of NCBITax:7955 zfa.obo > zfa_xp.obo~~
−
−	~~(TODO: add oboedit function to do this)~~
−
−	~~The script can be downloaded here:~~
−	http://~~geneontology.cvs.sourceforge.net/geneontology/go-dev/go-perl/scripts/obo-promote-dbxref-to-intersection.pl?view=log~~
−
−	~~Here is a section of the output:~~
−
−	~~[Term]~~
−	~~id: ZFA:0000134~~
−	~~name: neurons~~
−	~~namespace: zebrafish_anatomy~~
−	~~xref_analog: ZFIN:ZDB-ANAT-010921-563~~
−	~~xref_analog: CL:0000540~~
−	~~intersection_of: CL:0000540~~
−	~~intersection_of: part_of NCBITax:7955~~
−	~~relationship: end ZFS:0000044 ! Adult~~
−	~~relationship: part_of ZFA:0000396 ! nervous system~~
−	~~relationship: start ZFS:0000026 ! Segmentation:14-19 somites~~
−
−	~~All the script does is add intersection_of lines, which constitute the genus-differentia definition~~
−
−	~~We can feed the new file (zfa_xp.obo) to the reasoner~~
−
−	~~=Using the reasoner=~~
−
−	~~This section assumes use of the oboedit reasoner. See below for other reasoners~~
−
−	~~Load up 3 files into oboedit~~
−
−	~~- zfa_xp.obo (or whatever the SCA is) -- must include '''intersection_of''' lines (see above)~~
−	~~- cell.obo~~
−	~~- zf_taxonomy.obo~~
−
−	See above for the taxonomy file. The only thing that needs to be there is an entry for ZFA:7955. Having the full taxonomy may slow down the reasoner (TODO:test) - however, we may want to try this for projects such as CToL, where we want to reason over multiple related species - but let's keep this simple for now.
−
−	~~Turn on the reasoner. Exploring the DAG, you will see things like this:~~
−
−	~~[[Image:zfa_cell_align.jpg]]~~
−
−	The blue squiggly line between "primary interneurons" and "neurons" indicates the reasoner infers the existence of an (unasserted) is_a link. What should the SCA editor do here? They should make "primary interneurons" an is_a child of "neurons" (remember, although it looks like it is in the display, the blue squiggly line means it is 'inferred'). If the ZFA editor disagrees with this call, they should work with the CL editors to resolve this in CL. The only reason for neither CL or ZFA to amend their ontologies is if the two terms refer to different kinds of entity in reality. If this is the case, the explicit link between the two terms should be removed, and the priniciple of [[Univocity]] dictates that either CL or ZFA should change the name of one of their terms.
−
−	The straight red line indicates that an 'is_a' link has previously been asserted by the ZFA, and oboedit is showing that had the link not been asserted, it would have been able to figure it out from CL anyway. No action is required on the part of either ZFA or CL editors.
−
−	~~TODO: fill in section on using oboedit queries to find all inconsistencies~~
−
−	~~TODO: docs on using obo2obo to automoatically fill in is_a links, requiring no interaction on the part of the editor.~~
−
−	Note that the oboedit reasoner is intended for more complicated inferences than simply checking two types that refer to roughly the same entity are in sync (for example, GO processes that refer to CL). However, it works well enough for this simpler use-case.
−
−	~~==Pre-reasoned results==~~
−
−	* [http://www.berkeleybop.org/~~obol/#zebrafish_anatomy_xp_cell-obol ZFA to CL]~~
−	* [http://~~www.berkeleybop~~.~~org/obol~~/~~#po_anatomy_xp_cell-obol Plant anatomy (PO) to~~ CL]
−	* [http:~~//www.berkeleybop.org/obol/#fly_anatomy_xp_cell~~-~~obol Fly anatomy to CL]~~
−
−
−	~~==Other reasoners==~~
−
−	~~Since most SCAs are edited using oboedit, the oboedit reasoner will be the tool of choice for maintaining consistency between their ontologies and CL/CARO~~
−
−	~~It is worth noting that other editing tools and reasoners can be used - for example Protege-OWL or SWOOP could be used as the editor, and Pellet or FaCT++ could be used as the reasoner.~~
−
−	~~To do this with an obo ontology, you'd need to convert to OWL~~
−	~~See [[OboInOWL:Main_Page]]~~

← Older revision		Revision as of 20:27, 9 August 2007
Line 121:		Line 121:

	Note that the oboedit reasoner is intended for more complicated inferences than simply checking two types that refer to roughly the same entity are in sync (for example, GO processes that refer to CL). However, it works well enough for this simpler use-case.		Note that the oboedit reasoner is intended for more complicated inferences than simply checking two types that refer to roughly the same entity are in sync (for example, GO processes that refer to CL). However, it works well enough for this simpler use-case.
		+
		+	==Pre-reasoned results==
		+
		+	* [http://www.berkeleybop.org/obol/#zebrafish_anatomy_xp_cell-obol ZFA to CL]
		+	* [http://www.berkeleybop.org/obol/#po_anatomy_xp_cell-obol Plant anatomy (PO) to CL]
		+	* [http://www.berkeleybop.org/obol/#fly_anatomy_xp_cell-obol Fly anatomy to CL]
		+

	==Other reasoners==		==Other reasoners==

@@ Line 108: / Line 108: @@
 See above for the taxonomy file. The only thing that needs to be there is an entry for ZFA:7955. Having the full taxonomy may slow down the reasoner (TODO:test) - however, we may want to try this for projects such as CToL, where we want to reason over multiple related species - but let's keep this simple for now.
-Turn on the reasoner.
+Turn on the reasoner. Exploring the DAG, you will see things like this:
 [[Image:zfa_cell_align.jpg]]

@@ Line 74: / Line 74: @@
 (TODO: add oboedit function to do this)
 Here is a section of the output:
@@ Line 89: / Line 92: @@
    relationship: start ZFS:0000026 ! Segmentation:14-19 somites
-We can feed the new file to the reasoner
+All the script does is add intersection_of lines, which constitute the genus-differentia definition
 =Using the reasoner=

@@ Line 1: / Line 1: @@
 The OBO Cell ontology is intended to be a species-neutral reference ontology.
@@ Line 10: / Line 9: @@
 This assertion is universally true (all Purkinje cells are part_of some cerebellum at all times). The fact that not all organisms have a cerebellum is irrelevant. See [[RO:part_of]] for details.
-Here is the problem. We have a species-neutral cell ontology with Purkinje_cell (CL:0000121), but we have no species-neutral anatomy ontology with brain parts. We do have for example the zebrafish anatomy [[ZFA:Main_Page]] which has ZFA:0000100 cerebellum. So we can say:
+Here is the problem. We have a species-neutral cell ontology with Purkinje_cell (CL:0000121), but we have no
    CL:0000121 part_of ZFA:0000100
@@ Line 22: / Line 22: @@
 SCA curators may have other reasons for replicating CL terms (or terms from other species-neutral reference ontologies like GO) in their ontology.
-It's important that SCAs stay in sync with species neutral resources like CL and CARO [[CARO:Main_Page]]
+It's important that SCAs stay in sync with species neutral resources like CL and CARO [[CARO:Main_Page]]. This can be done automatically. First the SCA editors must maintain links to the CL; then they can use a reasoner to keep the ontologies in sync.