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aechchiki / BgeeDB_wdir

Add new ontologies for non-model species with RNA-seq annotated to be released in Bgee14
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stages to annotate: non-model Droso #7

Open aechchiki opened 8 years ago

aechchiki commented 8 years ago

7217: D. ananassae SRX247000 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX247001 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054476 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054477 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage

7230: D.mojavensis SRX017458 - info: Day 7 24h - mapped on FBdv:00007083 day 8 of adulthood SRX017459 - info: Day 7 24h - mapped on FBdv:00007083 day 8 of adulthood SRX017460 - info: Day 7 24h - mapped on FBdv:00007083 day 8 of adulthood SRX017461 - info: Day 7 24h - mapped on FBdv:00007083 day 8 of adulthood SRX054484 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054485 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054486 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054487 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage

7237: D. pseudobscura SRX016182 - info: Day 7 24h - mapped on FBdv:00007083 day 8 of adulthood SRX016183 - info: Day 7 24h - mapped on FBdv:00007083 day 8 of adulthood SRX054480 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054481 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054482 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054483 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091556 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091557 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091558 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091559 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091560 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091561 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091562 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091563 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage

7240: D. simulans SRX054463 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054464 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054465 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054466 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054467 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054468 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054469 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054470 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091564 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091565 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091566 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091567 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091568 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091569 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091570 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091571 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX091572 - info: 5-8 days post eclosion - mapped on FBdv:00007026 mature adult stage

7244: D. virilis SRX247002 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX247003 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054488 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054489 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage

7245: D. yakuba SRX246998 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX246999 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054472 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage SRX054473 - info: 5-7 days post eclosion - mapped on FBdv:00007026 mature adult stage

aechchiki commented 8 years ago

Info on sexual maturity:

aechchiki commented 8 years ago

ontology structure for new Drosophila spp:

[Term] name: Dxxx life cycle stage id: DxxxDv:00000000 xref: UBERON:0000105

[Term] name: Dxxx life cycle id: DxxxDv:0000001 xref: FBdv:00000000 xref: UBERON:0000104 is_a: DxxxDv:00000000 ! Dxxx life cycle stage

[Term] id: DxxxDv:00000002 name: embryonic stage xref: FBdv:00005289 xref: UBERON:0000068 is_a: DxxxDv:00000000 ! Dxxx life cycle stage relationship: part_of DxxxDv:0000001 ! Dxxx life cycle

[Term] id: DxxxDv:00000003 name: larval stage xref: FBdv:00005336 xref: UBERON:0000069 is_a: DxxxDv:00000000 ! Dxxx life cycle stage relationship: part_of DxxxDv:0000001 ! Dxxx life cycle relationship: immediately_preceded_by DxxxDv:00000002 ! embryonic stage

[Term] id: DxxxDv:00000004 name: P-stage xref: FBdv:00007001 xref: UBERON:0000070 is_a: DxxxDv:00000000 ! Dxxx life cycle stage relationship: part_of DxxxDv:0000001 ! Dxxx life cycle relationship: immediately_preceded_by DxxxDv:00000003 ! larval stage

[Term] id: DxxxDv:00000005 name: adult stage xref: FBdv:00005369 xref: UBERON:0018241 is_a: DxxxDv:00000000 ! Dxxx life cycle stage relationship: part_of DxxxDv:0000001 ! Dxxx life cycle relationship: immediately_preceded_by DxxxDv:00000004 ! P-stage

[Term] id: DxxxDv:00000006 name: immature adult stage xref: FBdv:00007025 xref: UBERON:0000112 is_a: DxxxDv:00000000 ! Dxxx life cycle stage relationship: part_of DxxxDv:0000001 ! Dxxx life cycle relationship: part_of DxxxDv:0000005 ! adult stage

[Term] id: DxxxDv:00000007 name: mature adult stage xref: FBdv:00007026 xref: UBERON:0000113 is_a: DxxxDv:00000000 ! Dxxx life cycle stage relationship: part_of DxxxDv:0000001 ! Dxxx life cycle relationship: part_of DxxxDv:0000005 ! adult stage relationship: immediately_preceded_by DxxxDv:00000006 ! immature adult stage

@ANiknejad do you think this structure is correct? :)

ANiknejad commented 8 years ago

review of FBdv annotation in current 'affymetrixChip.tsv' (you gave me on 27 June via USB key), thus it might be supposed that the same annotation will be used for other Droso species, even if you listed above (first post) the current available experiments. Here the list of current Affy Drosophila melanogaster stage annotation, with comment

FBdv:00000000 ---> 3 annotations, should be on FBdv:00005369 adult stage, instead TO CORRECT FBdv:00000054 cleavage stage FBdv:00004450 late extended germ band stage FBdv:00004886 oogenesis stage FBdv:00005283 oogenesis stage S14 FBdv:00005287 unfertilized egg stage FBdv:00005289 embryonic stage FBdv:00005290 pre-blastoderm stage FBdv:00005293 embryonic stage 2 FBdv:00005306 embryonic stage 4 FBdv:00005309 embryonic cycle 13 FBdv:00005311 embryonic stage 5 FBdv:00005312 embryonic cycle 14 FBdv:00005321 extended germ band stage FBdv:00005324 embryonic stage 10 FBdv:00005327 embryonic stage 12 FBdv:00005331 dorsal closure stage FBdv:00005332 embryonic stage 15 FBdv:00005335 embryonic stage 17 FBdv:00005336 larval stage FBdv:00005337 first instar larval stage FBdv:00005338 second instar larval stage FBdv:00005339 third instar larval stage FBdv:00005340 early third instar larval stage FBdv:00005341 wandering third instar larval stage FBdv:00005342 prepupal stage FBdv:00005343 prepupal stage P1 FBdv:00005364 pharate adult stage P13 FBdv:00005369 adult stage FBdv:00007001 P-stage FBdv:00007005 third instar larval stage L2 FBdv:00007007 late third instar larval stage FBdv:00014201 early extended germ band stage

review of current annotation into 'RNASeqLibrary.tsv' (you gave me on 27 June via USB key)

FBdv:00007078 Day 3 of adulthood FBdv:00007085 day 10 of adulthood FBdv:00007079 day 4 of adulthood FBdv:00007083 day 8 of adulthood FBdv:00007026 mature adult stage UBERON:0004730 larval stage

ANiknejad commented 8 years ago

relationship: part_of DxxxDv:0000001 ! Dxxx life cycle relationship: part_of DxxxDv:0000005 ! adult stage

--> please remove relationship: part_of DxxxDv:0000001 ! Dxxx life cycle when the class is already part_of another parent class

aechchiki commented 8 years ago

ok! done.

Droso ontologies with the specified ontology structure are in: https://github.com/aechchiki/developmental-stage-ontologies/tree/master/src (fork of the original repo)

aechchiki commented 8 years ago

@ANiknejad

In: https://github.com/aechchiki/developmental-stage-ontologies/tree/master/src The complete ontologies for new species are in their folders:

The file .tsv containing the NCBI taxon ID, as required by Fred, are also in their folders.

ANiknejad commented 8 years ago

some comments:

details, in cpordv.obo please change 'aprox' by 'approx'

in DmojDv please correct typo lines 9,17 also a space to remove in front of lines 22, 41

ANiknejad commented 8 years ago

DsimDv, DvirDv remove a space in front of line 22

DyakDv idem, lines 32, 75

ANiknejad commented 8 years ago

did you load the ontologies into OboEdit? should crash with such typo errors, maybe good to load each of the ontologies to be sure about the structure, please let me know if there is an issue usign OboEdit @aechchiki

aechchiki commented 8 years ago

thanks. it is fixed! commit: https://github.com/aechchiki/developmental-stage-ontologies/commit/49ba868e83f0c4368d7a487a81b3a890520b105a

For OBOEdit, I find it a bit weird to use it to construct ontologies. I use a plain text editor instead. but you are right, I have to test the ontologies in OBOEdit after having written them in plain text editor.

I was wondering if we also have to add a new term (adult day 7) for:

These are the only two species with some experiments with precision "Day 7 24h". otherwise there is no more detail to allow mapping on other terms than "mature adult"

ANiknejad commented 8 years ago

thank you, Amina yes, I also only use OboEdit to check the ontology at the end, not to create or edit it.

ANiknejad commented 8 years ago

https://books.google.ch/books?id=OfYOU8liOn0C&printsec=frontcover#v=onepage&q=sexual%20maturity&f=false

this book should have the information we are looking for regarding sexual maturity over Drosophila species..sounds like not available at our lab... http://wiki.isb-sib.ch/mrrwiki/Books could you anyway check if sitting on my desk or directly with Marc?

ANiknejad commented 8 years ago

I was wondering if we also have to add a new term (adult day 7) for:

D.mojavensis
D. pseudobscura

These are the only two species with some experiments with precision "Day 7 24h". otherwise there is > no more detail to allow mapping on other terms than "mature adult"

I guess, we only can consider 'adult stage' for Drosophila species, because FBdv:00007025 immature adult stage and FBdv:00007026 mature adult stage

do NOT REFER to sexual maturity, as this is the case for the Uberon classes UBERON:0000112 sexually immature stage UBERON:0000113 post-juvenile adult stage