Difference between zebrafish ontology from Melissa and from Bgee

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The difference concerns the hatching period. 

In Melissa's ontology: 
- pharyngula
...
-- Hatching:Long-pec
- larva
-- Hatching:Pec-fin

In Bgee's ontology: 
- embryonic stage
-- hatching period
--- hatching:long-pec stage
--- hatching stage at 52 hpf 
--- hatching stage at 56 hpf 
--- hatching:pec-fin stage

So there are two differences:

1) Addition of the terms "hatching stage at 52 hpf" and "hatching stage at 56 
hpf" in Bgee. 
They correspond to terms often used in publications, but missing in the ZFA 
ontology. See 
http://zfin.org/cgi-bin/webdriver?MIval=aa-fxallfigures.apg&OID=ZDB-PUB-090929-9
 for an example.

2) In Melissa's ontology, "Hatching:Pec-fin" is a larval stage, while all 
hatching stages are embryonic stages in Bgee. 
It seems that a hatching individual is considered to be an embryo: 
'Whether or not an embryo has hatched, its development progresses, hour by 
hour, and generally individuals that have spontaneously hatched are not more 
developmentally advanced that ones remaining in their chorions. We arbitrarily 
call the creatures "embryos" until the end of the third day, and afterwards, 
"larvae", whether they have hatched or not (Fig. 39). '

http://zfin.org/zf_info/zfbook/stages/hatch.html

This seems consistent with the classical definition of the embryonic stage in 
zebrafish, covering the first three days of development: 
http://zfin.org/zf_info/zfbook/stages/phar.html

Original issue reported on code.google.com by TheITGuy...@gmail.com on 5 Feb 2013 at 8:59

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Hi All,

any comments on this issue? do you plan to do changes in ZFS?

thank you in advance

Best regards,

Anne

Original comment by niknej...@gmail.com on 4 Sep 2014 at 12:31

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So far there has been no discussion of subdividing the Long-Pec stage through 
the addition of hatching stages at 52 and 56 hpf. The staging is representative 
of the Hatching Period as described here 
http://zfin.org/zf_info/zfbook/stages/hatch_stgs.html The current state of the 
ZFS has worked well for ZFIN curators and they have not expressed a need to 
further subdivide the staging. Can you please explain your need for this change?
The addition of the term ‘Hatching’ stage could be added to the ontology to 
better represent the subdivision of the stages as represented here 
http://zfin.org/zf_info/zfbook/stages/index.html This would allow for the 
stages Long-Pec, Pec-fin and Protruding mouth to be grouped under the 
‘Hatching’ stage as described. 

Original comment by ybradf...@zfin.org on 4 Sep 2014 at 9:11

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Hello,
Many thanks for your quick answer.
We annotate expression data reported in GEO, please have a look at this 
experiment:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5048
Here there are data at embryo stage 52hpf. We consider this period of time as 
belonging to 'Hatching (48 - 72 h)'
'52hpf' and '56hpf' sound to be usual milestones for experiment in literature, 
please see also http://www.ncbi.nlm.nih.gov/pubmed/?term=24504339
for in situ expression.

Yes, addition of a 'hatching stage' is a good idea, thank you in advance. We 
will request a corresponding term to Uberon, as soon as you provide a nice 
definition for this term.

Thank you again for all your efforts and your responsiveness.

Best regards,

Anne

Original comment by niknej...@gmail.com on 8 Sep 2014 at 8:36

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I've added hatching stage to ZFS. There has been no decision as of yet to add 
the child terms 52hpf and 56hpf to the ontology.

Original comment by ybradf...@zfin.org on 25 Sep 2014 at 9:23

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Many thanks, Yvonne, for adding hatching stage to ZFS.
Could you please let me know when a (zfa.obo) release is planned?
Best regards,

Anne

Original comment by niknej...@gmail.com on 13 Oct 2014 at 4:07

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The ZFA will release in early November.  The changes to the ZFS are in the 
standalone file and will not be visible in the ZFA.

Original comment by zfinf...@gmail.com on 21 Oct 2014 at 4:49