development standard definition implementation

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Hi,

I'm going to implement these standard definitions soon. They've been agreed already by the development interest group. I'm posting them here in case anybody'd like to comment on the detailed wording before I implement them.

"x" development Processes aimed at the progression of the "x" over time, from its formation to the mature structure.

"x" morphogenesis Processes by which the anatomical structures of "x" are generated and organized. Morphogenesis pertains to the creation of form.

"x" formation Processes that contribute to the act of giving rise to "x". This process pertains to the initial formation of a structure from unspecified parts.

Thanks,

Jen

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/1841":https://sourceforge.net/p/geneontology/ontology-requests/1841

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I have added defs to some terms where there was no def at all. Amelia is working on writing a script to deal with the straightforward terms. The morphogenesis terms are going to be a problem because many of them
are defined 'the formation and development of...', which is basically saying that although the term claims to be a morphogenesis term, it's actually defined as a development term. This means that if I change these defs to be the new standard morphogenesis defs then the concept being defined will be changing from what was a development term to what is now a morphogenesis term. I can't do that, and so Midori and I worked out that I can either change the morphogenesis term to be a development term and have the name 'x development' and the standard development def, and appropriate position in the graph, or I can just merge the term into the pre-existing development term where there is one.

Jen

Original comment by: jenclark

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e-mailed David about the morphogenesis problem:

Hi David,

I've just started putting in the revised standard defs for development morphogenesis and formation terms. I discovered that many of the morphogenesis terms are defined 'the formation and development of...' This means that if I change these defs to be the new standard morphogenesis defs then the concept being defined will be changing from what was actually a development term to what is now a morphogenesis term. I can't do that, and so Midori and I worked out that I can either change the morphogenesis term to be a development term and have the name 'x development' and the standard development def, and appropriate position in the graph, or I can just merge the term into the pre-existing development term where there is one. Does this seem reasonable to you? There are an awful lot of these terms, but I think it has to be done to get the development node to really say what it thinks it's saying.

Second opinion much appreciated.

Thanks,

Jen

His reply:

That's funny. I just noticed that this morning with eye morphogenesis (sensu mammalia). The def of this term actually describes eye development. I think these errors are historical because originally we used the terms development and morphogenesis interchangeably without having a formal definition for either concept. But, changing "eye morphogenesis (sensu mammalia)" to "eye development (sensu mammalia)" doesn't solve the problem, because certainly "eye morphogenesis (sensu mammalia)" should be a term under organogenesis (actually right where it is in the graph). I think the best way to solve this would be to:

1) create an "development of an organ" term. 2) move all of the current morphogenesis terms that have development definitions out to be children of this term and change their name to be XYZ development. 3) for all of those that have moved, create a new XYZ morphogenesis term that would replace the ones that were moved and changed. Retain the parent relationships of those new terms as they are in the current graph. This is because the current morphogenesis terms fit right with respect to the graph, just not with respect to their definitions.

These will be big changes, so I think it should go out to the development group, some of whom I've included on this email. We also need to document this!

David

My reply:

Hi David,

Yes I see what you mean. Many of the morphogenesis terms that are currently defined as development terms will be just as complicated to fix but will require different solutions.

Shall I just do them slowly one at a time, with sourceforge items so people can discuss what to do in each case? I think it's important to get these right so there is no longer this confusion between morphogenesis and development. I don't know the background of a lot of these terms so it would be really helpful if people could chip in with ideas and background information as it's required.

For added amusement, I see that some of the 'x formation' terms are defined 'morphogenesis of x' but there are far fewer of those so that's not nearly such a huge workload to sort out.

I'm not quite sure how to document this effectively so if anybody has good ideas I'd be interested to know. I could just add a section tot he development documentation to say that this rearrangement was carried out and that the morphogenesis terms that had previously been defined as development terms were dealt with on a case by case basis, as discussed in the sourceforge tracker.

While I'm here, the development documentation is ready for proof-reading if anybody has a spare minute to send comments. http://www.ebi.ac.uk/~jclark/GOwebsite/development\_folder/ GO.process.guidelines.html

Thanks,

Jen

Original comment by: jenclark

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Becky's thoughts:

(I'm pasting all this in because it's not going to the list so not being archived.)

Hi David,

This proposal looks ok to me I think- I need to play in DAG-Edit and do some reading to work out how to fit the fly development/morphogenesis terms in with the imaginal disc terms. And which of the current terms belong under eye morphogenesis, and which under eye development.

Do we need to do anything with all the X development terms that are currently under organogenesis? eg:

development ; GO:0007275 --%morphogenesis ; GO:0009653 ----%organogenesis ; GO:0009887 ------%heart development ; GO:0007507 ------%muscle development ; GO:0007517 ------%notochord development ; GO:0030903 ------%skeletal development ; GO:0001501 ------%urogenital system development ; GO:0001655 etc etc

Becky

Then me:

Can we really just move them all out to be children of 'development of an organ'?

It seem to me that they're not all organs e.g.

body morphogenesis bristle morphogenesis ectodermal gut morphogenesis

What do you mean by 'organ'?

Thanks,

jen

Original comment by: jenclark

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Amelia is writing a script that will implement standard definitions where possible for the morphogenesis and development terms. The complicated ones will be done by me by hand. Below is the text I sent her as a basis for the script. (Also uploaded as a text file.)

The following are 'x development' terms that can have the def generated straight from the standard definition:

0001541 0001655 0001657 0007418 0007419 0007422 0007423 0007497 0007522 0008544 0010214 0035050 0048366 0048367 0048368 0048413 0048437 0048438 0048441 0048442 0048443 0048464 0048465 0048466 0048467 0048468

The following are 'x development' terms that can have the def generated straight from the standard definition but then need to have a sensu ending attached as well. (I have included the sensu term name and def endings below.)

0001749 0002117 0048409 0048417 0048421 0048425 0048433 0048440

The following are 'x development' terms that can have the def generated straight from the standard definition but only the first sentence of the current definition should be replaced. The rest of the definition needs to be kept.

0001748 0002164 0007398 0007492 0007498 0007502 0007503 0007504 0007506 0007508 0007516 (has sensu ending) 0030324 0048316 0048318 0048339 0048364 0048382 0048383 0048389

The following are 'x morphogenesis' terms that can have the def generated straight from the standard definition.

0007437 0007441 0008407 0009965 0035136 0035137 0048317 0048319 0048332 0048340 0048369 0048390 0048439 0048444 0048445 0048446 0048447 0048448 0048457

The following are 'x morphogenesis' terms that can have the def generated straight from the standard definition but need the sensu ending added.

0048411 0048414 0048418 0048422 0048426 0048430 0048434

The following are 'x morphogenesis' terms that can have the def generated straight from the standard definition but only the first sentence of the def should be replaced and the rest needs to be kept.

0007443 0035138 0035139 0035140 0035141 0035142 0035143 0035144

This is the standard definition:

Term name: x development def: Processes aimed at the progression of the x over time, from its formation to the mature structure.

Term name: x morphogenesis def: Processes by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form.

These are the sensu term names and def endings:

Term name ends: (sensu Amphibia) def ends: As in, but not restricted to, the amphibia (Amphibia, ncbi_taxonomy_id:8292). Term name ends: (sensu Eubacteria) def ends: As in, but not restricted to, the taxon Eubacteria (Bacteria, ncbi_taxonomy_id:2). Term name ends: (sensu Cyanobacteria) def ends: As in, but not restricted to, the blue-green algae (Cyanobacteria, ncbi_taxonomy_id:1117). Term name ends: (sensu Dictyosteliida) def ends: As in, but not restricted to, the taxon Dictyosteliida (Dictyosteliida, ncbi_taxonomy_id:33083). Term name ends: (sensu Diptera) def ends: As in, but not restricted to, the true flies (Diptera, ncbi_taxonomy_id:7147). Term name ends: (sensu Drosophila) def ends: As in, but not restricted to, the Genus Drosophila (Drosophila, ncbi_taxonomy_id:7215). Term name ends: (sensu Deuterostomia) def ends: As in, but not restricted to, the taxon Deuterostomia (Deuterostomia, ncbi_taxonomy_id:33511). Term name ends: (sensu Endopterygota) def ends: As in, but not restricted to, the Holometabola (Endopterygota, ncbi_taxonomy_id:33392). Term name ends: (sensu eudicotyledons) def ends: As in, but not restricted to, the dicotyledonous plants (eudicotyledons, ncbi_taxonomy_id:71240). Term name ends: (sensu Eukaryota) def ends: As in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759). Term name ends: (sensu Fungi) def ends: As in, but not restricted to, the fungi (Fungi, ncbi_taxonomy_id:4751). Term name ends: (sensu Gnetophyta) def ends: As in, but not restricted to, the taxon Gnetophyta (Gnetophyta, ncbi_taxonomy_id:58022). Term name ends: (sensu Insecta) def ends: As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557). Term name ends: (sensu Magnoliophyta) def ends: As in, but not restricted to, the flowering plants (Magnoliophyta, ncbi_taxonomy_id:3398). Term name ends: (sensu Mammalia) def ends: As in, but not restricted to, mammals (Mammalia, ncbi_taxonomy_id:40674). Term name ends: (sensu Metazoa) def ends: As in, but not restricted to, animals (Metazoa, ncbi_taxonomy_id:33208). Term name ends: (sensu Nematoda) def ends: As in, but not restricted to, the roundworms (Nematoda, ncbi_taxonomy_id:6231). Term name ends: (sensu Protostomia) def ends: As in, but not restricted to, the taxon Protostomia (Protostomia, ncbi_taxonomy_id:33317). Term name ends: (sensu Nematoda and Protostomia) def ends: As in, but not restricted to, the roundworms (Nematoda, tax ID:6231) and the taxon Protostomia (Protostomia, ncbi_taxonomy_id: 33317). Term name ends: (sensu Proteobacteria) def ends: As in, but not restricted to, the purple bacteria and relatives (Proteobacteria, ncbi_taxonomy_id: 1224). Term name ends: (sensu Saccharomyces) def ends: As in, but not restricted to, the taxon Saccharomyces (Saccharomyces, ncbi_taxonomy_id:4930). Term name ends: (sensu Tracheophyta) def ends: As in, but not restricted to, the vascular plants (Tracheophyta, ncbi_taxonomy_id:8023). Term name ends: (sensu Vertebrata) def ends: As in, but not restricted to, the vertebrates (Vertebrata, ncbi_taxonomy_id:7742). Term name ends: (sensu Viridiplantae) def ends: As in, but not restricted to, green plants and algae (Viridiplantae, ncbi_taxonomy_id:33090).

Original comment by: jenclark

[gocentral]

info for amelia about which defs can be changed by the script.

Original comment by: jenclark

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e-mail back from David on the moving morphogenesis terms thing:

No, not all of them. Just the ones that are organs should be moved. I actually think that a term like body development does not make sense. For a term like body morphogenesis, I think we really meant morphogenesis.

David

me:

Great, thanks. Is that okay then if I just stick proposals into sourceforge for each one and we can see what happens?

(Starting with eye morphogenesis)

Jen

Original comment by: jenclark

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I think we should look at their defs and move them without a name change if appropriate. NOte, that right now I think we should solve this problem for organogenesis and its children. I think the other terms under morphogenesis may need to be rearranged in other ways. As I pointed out in my last email. I really think we meant body morphogenesis when we made that term, despite its definition.

David

Hi David,

> I think we should look at their defs and move them without a name change if appropriate. NOte, that right now I think we should solve this problem for organogenesis and its children.

Okay We could do all the organogenesis terms first.

I think the other terms

> under morphogenesis may need to be rearranged in other ways. As I pointed out in my last email. I really think we meant body morphogenesis when we made that term, despite its definition.

Yes that's fine too. I think that whatever was intended when the term was made we need to assume that people will have annotated to the definition. That means that if a term that was intended to be morphogenesis but was defined as development then it needs to be merged into a development term or obsoleted with a comment to reannotate to the replacement morphogenesis term (which would actually be defined as morphogenesis.).

Jen

Original comment by: jenclark

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The morphogenesis terms that are also children of organogenesis are now being discussed in [ 990247 ] organ morphogenesis terms https://sourceforge.net/tracker/index.php? func=detail&aid=990247&group_id=36855&atid=440764

Jen

Original comment by: jenclark

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Defs standardized: chlamydospore formation (sensu Candida albicans), GO:0001410 hyphal tip, GO:0001411 ovarian follicle development, GO:0001541 urogenital system development, GO:0001655 ureteric bud development, GO:0001657 Bolwig's organ morphogenesis, GO:0001746 optic placode development (sensu Drosophila), GO:0001748 non-eye photoreceptor development (sensu Drosophila), GO:0001749 larval development (sensu Amphibia), GO:0002117 larval development, GO:0002164 ectoderm development, GO:0007398 sensory organ development, GO:0007423 adult salivary gland morphogenesis, GO:0007437 foregut morphogenesis, GO:0007440 anterior midgut (ectodermal) morphogenesis, GO:0007441 hindgut morphogenesis, GO:0007442 Malpighian tubule morphogenesis, GO:0007443 endoderm development, GO:0007492 mesoderm development, GO:0007498 gut mesoderm development, GO:0007502 fat body development, GO:0007503 larval fat body development, GO:0007504 gonadal mesoderm development, GO:0007506 larval heart development, GO:0007508 hemocyte development, GO:0007516 bristle morphogenesis, GO:0008407 epidermis development, GO:0008544 leaf morphogenesis, GO:0009965 seed coat development, GO:0010214 lung development, GO:0030324 embryonic heart tube development, GO:0035050 forelimb morphogenesis, GO:0035136 hindlimb morphogenesis, GO:0035137 pectoral fin morphogenesis, GO:0035138 pelvic fin morphogenesis, GO:0035139 arm morphogenesis, GO:0035140 medial fin morphogenesis, GO:0035141 dorsal fin morphogenesis, GO:0035142 caudal fin morphogenesis, GO:0035143 anal fin morphogenesis, GO:0035144 seed development, GO:0048316 seed morphogenesis, GO:0048317 axial mesoderm development, GO:0048318 axial mesoderm morphogenesis, GO:0048319 mesoderm morphogenesis, GO:0048332 paraxial mesoderm development, GO:0048339 paraxial mesoderm morphogenesis, GO:0048340 root development, GO:0048364 leaf development, GO:0048366 shoot development, GO:0048367 lateral mesoderm development, GO:0048368 lateral mesoderm morphogenesis, GO:0048369 mesendoderm development, GO:0048382 mesectoderm development, GO:0048383 intermediate mesoderm development, GO:0048389 intermediate mesoderm morphogenesis, GO:0048390 flower development (sensu eudicotyledons), GO:0048409 flower morphogenesis (sensu eudicotyledons), GO:0048411 floral whorl development (sensu eudicotyledons), GO:0048413 floral whorl morphogenesis (sensu eudicotyledons), GO:0048414 petal development (sensu eudicotyledons), GO:0048417 petal morphogenesis (sensu eudicotyledons), GO:0048418 sepal development (sensu eudicotyledons), GO:0048421 sepal morphogenesis (sensu eudicotyledons), GO:0048422 stamen development (sensu eudicotyledons), GO:0048425 stamen morphogenesis (sensu eudicotyledons), GO:0048426 carpel morphogenesis (sensu eudicotyledons), GO:0048430 floral organ development (sensu eudicotyledons), GO:0048433 floral organ morphogenesis (sensu eudicotyledons), GO:0048434 floral organ development, GO:0048437 floral whorl development, GO:0048438 flower morphogenesis, GO:0048439 carpel development, GO:0048440 petal development, GO:0048441 sepal development, GO:0048442 stamen development, GO:0048443 floral organ morphogenesis, GO:0048444 carpel morphogenesis, GO:0048445 petal morphogenesis, GO:0048446 sepal morphogenesis, GO:0048447 stamen morphogenesis, GO:0048448 floral whorl morphogenesis, GO:0048457 calyx development, GO:0048464 corolla development, GO:0048465 androecium development, GO:0048466 gynoecium development, GO:0048467 cell development, GO:0048468

Original comment by: girlwithglasses

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Great, thanks. :-) That was super fast too.

There's a couple of unexpected ones there but they haven't been changed by the script, so that's fine.

(chlamydospore formation (sensu Candida albicans), GO:0001410 hyphal tip, GO:0001411)

Thanks for the help with this. :-)

Jen

Original comment by: jenclark

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All the 'x' development terms are done now.

Jen

Original comment by: jenclark

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I have done the morphogenesis terms in alphabetical order up to the end of the embryonic morphogenesis terms. I skipped those that require anything more major than a rewording of the definition.

Jen

Original comment by: jenclark

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I have now added the standard definitions to all the morphogenesis terms that did not include the word 'development' in the current definition. They will need more complicated work to sort them out.

Original comment by: jenclark

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I have made a filter in dag-edit that finds only the morphogenesis terms that still need some work. I couldn't work out how to export them so I just took a snapshot and have uploaded them at the bottom here as morph.jpg and morph1.jpg.

Jen

Original comment by: jenclark

[gocentral]

morphogenesis terms that still need work. 29/7/4

Original comment by: jenclark

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the bits that weren't in the picture in morph.jpg

Original comment by: jenclark

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The development terms are done and the morphogenesis terms are covered under other items so I will close this.

for morphogenesis terms see:

1101748 standardizing morphogenesis terms 1065289 organ morphogenesis terms 2

for formation terms see:

1146293 standardizing formation terms

Thanks,

Jen

Original comment by: jenclark

[gocentral]

• status: open --> closed-accepted

Original comment by: jenclark