大切 FALDO paper will go to preprint at 01:00 tonight (10:00 JST Tomorrow)

[Jerven Bolleman]

Hi All,

I would like to submit the current preprint to biorxiv tonight. You
have 14 hours to say no. Otherwise I assume ok given earlier e-mails.

Current PDF attached.

So deadline for disagreement is

Thursday, 30 January 2014, 10:00:00 JST (Tokyo)
Thursday, 30 January 2014, 01:00:00 CET (Bern)


Regards,
Jerven

--
Jerven Bolleman
m...@jerven.eu

[Peter Cock]

On Wed, Jan 29, 2014 at 10:00 AM, Jerven Bolleman <m...@jerven.eu> wrote:
> Hi All,
>
> I would like to submit the current preprint to biorxiv tonight. You
> have 14 hours to say no. Otherwise I assume ok given earlier e-mails.
>
> Current PDF attached.
>
> So deadline for disagreement is
>
> Thursday, 30 January 2014, 10:00:00 JST (Tokyo)
> Thursday, 30 January 2014, 01:00:00 CET (Bern)
>
>
> Regards,
> Jerven

Thank you Jerven,

I'm happy for you to submit this to http://bioRxiv.org tonight.

I like the new sentence you added for historical context:
https://github.com/JervenBolleman/FALDO-paper/commit/d8188c8d36e9ae60eedaf2bc34a410f5403d8b6c

Do you think is it ready for submission to the Journal of Biomedical
Semantics as well?

The only open issue is to add a bit of information about which
version of BioPerl included the FALDO exporter, which is
something we could easily add later during the review process.

Regards,

Peter

[Jerven Bolleman]

Hi All,

I am happy to submit it to the Journal of Biomedical Semantics as
well. I will need to write a cover letter, and looking at the error
logs of uniprot production I don't think that is going to happen today
:(

Secondly I forgot to ask can every author send the e-mail they want
the Biomed Central to use and Orcid ID's if you have them.

Regards,
Jerven

--
Jerven Bolleman
m...@jerven.eu

[Toshiaki Katayama]

Hi Jerven,

Thank you for the Japanese subject! :)

Sorry for that I could not reply to the thread as I'm running a domestic version of BioHackathon this week in Okinawa, Japan.
I just have finished reading through a bunch of emails on FALDO and mostly happy with the result of recent discussions and progress.
If I missed something to respond, please let me know.

I'll try to read through the final manuscript tomorrow morning (if I could have one more day for this, it would help me) but here are few points before I go to sleep:

The CC0 licence is fine with me. Also, thank you for including BH series in Acknowledgements. In acknowledgements, could you update

* s/Biohackathon/BioHackathon/g ?
* s/This work and Toshiaki Katayama were supported/The BioHackathon series, this work and Toshiaki Katayama were supported/

Note that as I commented on GitHub at https://github.com/JervenBolleman/FALDO-paper/pull/25#issuecomment-33585011 I'm now working on a VCF to RDF converter in the BioInterchange code base during this domestic BioHackathon (I'm not sure if I will finish the work by the end of this week though).

Good night.

Regards,
Toshiaki

2014/01/29 19:41、Jerven Bolleman <m...@jerven.eu> のメール：

> --
> You received this message because you are subscribed to the Google Groups "FALDO" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to faldo+un...@googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.

[Peter Cock]

On Wed, Jan 29, 2014 at 4:48 PM, Toshiaki Katayama
<toshiaki...@gmail.com> wrote:
>
> ... Also, thank you for including BH series in Acknowledgements. In acknowledgements, could you update

>
> * s/Biohackathon/BioHackathon/g ?
> * s/This work and Toshiaki Katayama were supported/The BioHackathon series, this work and Toshiaki Katayama were supported/

Change applied:
https://github.com/JervenBolleman/FALDO-paper/commit/9625a305ecb4e0db7f96bceadab0ba1535cdb89a

Thanks,

Peter

[Jerven Bolleman]

Not a problem 24 hours extra ;)

Thank you very much for all your effort as well.

I just hope the japanese given by google translate was ok.

Regards,
Jerven

--
Jerven Bolleman
m...@jerven.eu

[Toshiaki Katayama]

Hi Jerven,

Thank you for giving us extra time!

Takatomo and I reviewed the manuscript based on the PDF file sent to this group yesterday.

I'll keep working on the sections indicated by [TODO] sign in below.


Here are our comments:

First of all, cases would be better to be consistent: s/semantic web/Semantic Web/g


p.4 Implementation

"i.e. something with an end and start position." -> "i.e. something with a start and end position."


p.5 Figure 1

Do we really need this negative phrase "for semantically poor data" here?


p.7 Users

"(see figure 5)" → "(see Figure 5)"


p.8 Figure 5

[TODO]
I hope to replace the figure with an updated version (in preparation).


p.13 Figure 9

The following URIs are not yet in production (pseudo) ones but please update from

"ddbj" : "http://.../exampleDDBJrecordNamespace/",
"ddbj-record" : "http://.../exampleDDBJrecordNamespace/" ,
"ddbj-seq" : "http://.../exampleDDBJsequenceNamespace/" ,

to

"ddbj" : "http://ddbj.nig.ac.jp/ontologies/sequence/",
"ddbj-record" : "http://ddbj.nig.ac.jp/entry/nucleotide/",
"ddbj-aa" : "http://ddbj.nig.ac.jp/entry/protein/",
"ddbj-seq" : "http://ddbj.nig.ac.jp/entry/sequence/",

and need to change "ddbj:CDS" to "ddbj:feature", so the resulted JSON will be as follows (with spaces before ',' and '"' are carefully removed)

{
"@context" : {
"label" : "http://www.w3.org/2000/01/rdf-schema#label",
"comment" : "http://www.w3.org/2000/01/rdf-schema#comment",
"taxonomy" : "http://purl.uniprot.org/taxonomy/",
"identifier" : "http://purl.org/dc/terms/identifier",
"ddbj" : "http://ddbj.nig.ac.jp/ontologies/sequence/",
"ddbj-record" : "http://ddbj.nig.ac.jp/entry/nucleotide/",
"ddbj-protein" : "http://ddbj.nig.ac.jp/entry/protein/",
"ddbj-seq" : "http://ddbj.nig.ac.jp/entry/sequence/",
"faldo" : "http://biohackathon.org/resource/faldo#",
"so" : "http://purl.obolibrary.org/obo/so.owl#"
},
"@id" : "ddbj-record:J02448",
"identifier" : "J02448",
"comment" : "Bacteriophage f1, complete genome",
"ddbj:organism" : "taxonomy:10863",
"ddbj:feature" : {
"@id" : "ddbj-protein:AAA32209.1",
"@type" : "so:0000316",
"label" : "Protein II",
"faldo:location" : {
"@type" : "faldo:Region",
"faldo:begin" : {
"@type" : [ "faldo:Position", "faldo:ExactlyKnownPosition", "faldo:ForwardStrandPosition" ],
"faldo:position" : "6006",
"faldo:reference" : "ddbj-seq:J02448"
},
"faldo:end" : {
"@type" : [ "faldo:Position", "faldo:ExactlyKnownPosition", "faldo:ForwardStrandPosition" ],
"faldo:position" : "831" ,
"faldo:reference" : "ddbj-seq:J02448"
}
}
}
}


p.10 Figure 6

Probably "isoform:P05064-1" should be replaced with "isoform:Q6Q250-1" as the subject ID is "uniprot:Q6Q250".


p.12 Figure 8

In the figure, "refseq:NC_000913.2" must be replaced with "ddbj:U00096.3" as RefSeq is not an INSDC database and please use the following prefix.

@prefix ddbj: <http://ddbj.nig.ac.jp/entry/nucleotide/> .

Also, the figure legend must be changed to

"Figure 8: Using FALDO in Turtle [27] syntax to describe the location of a gene feature cheY at complement(1965072..1965461) in a INSDC record U00096.3."

[TODO]
Do you have any specific reason to use "cheY" gene here? (or can I use other gene instead?)


p.15 Figure 10

How about to replace following URIs

":EnzymeRestrictionSite" -> ":enzymeRestrictionSite"
":EnzymeRestrictionRegion" -> ":enzymeRestrictionRegion"

as they are instances (not Classes)?

Also, I suspect assignment of locations of :53cleavageSite and :35cleaveageSite are wrongly inverted to each other maybe?

:enzymeRestrictionSite a example:EnzymeRestrictionSite ;
faldo:location :EnzymeRestrictionRegion .

:enzymeRestrictionRegion a faldo:Region ;
faldo:begin :53_1 ;
faldo:end :35_6 .

:53cleaveageSite a example:CleavageSite ;
faldo:location [a faldo:InBetweenPosition,
SO:0001689 ; # 5’ restriction enzyme junction
faldo:after :53_1 ;
faldo:before :53_2 ] .

:35cleaveageSite a example:CleavageSite ;
faldo:location [a faldo:InBetweenPosition,
SO:0001690 ; # 3’ restriction enzyme junction
#Note the before after reversion due to biological start
faldo:before :35_5 ;
faldo:after :35_6 ] .


p.14 Discussion

"This encoding means there is no need to know the length of the sequence to compare positions on the different strands."

This statement is not true for the case that "features overlap the chromosome's origin of replication" described in p.12 and Figure 9.



THAT'S IT!!


Regards,
Toshiaki



2014/01/30 7:03、Jerven Bolleman <m...@jerven.eu> のメール：

[Jerven Bolleman]

Thank you so much!
Will implement the changes right away and will make sure the DDBJ
URI's are changed in all figures.

Regards,
Jerven

--
Jerven Bolleman
m...@jerven.eu

[Jerven Bolleman]

First of all thank you! Takatomo-san and you have been great in picking up all these errors of mine!

Quick comments about TODO’s only

On 30 Jan 2014, at 13:08, Toshiaki Katayama <kt...@dbcls.jp> wrote:

> Hi Jerven,

> [TODO]
> I hope to replace the figure with an updated version (in preparation).

Let me know when you have it. For the journal of biomedical semantics my boss needs to approve the paper as well so you have time for the peer review one.

>
> "Figure 8: Using FALDO in Turtle [27] syntax to describe the location of a gene feature cheY at complement(1965072..1965461) in a INSDC record U00096.3."
>
> [TODO]
> Do you have any specific reason to use "cheY" gene here? (or can I use other gene instead?)

No specific reason just wanted a gene on the complement strand.

> p.14 Discussion
>
> "This encoding means there is no need to know the length of the sequence to compare positions on the different strands.”

> This statement is not true for the case that "features overlap the chromosome's origin of replication" described in p.12 and Figure 9.

Would this sentence work?
"This encoding means there is no need to know the length of the sequence to compare positions on the different strands on a linear chromosome or genome.”

[Toshiaki Katayama]

Hi Jerven,

[TODO]
I hope to replace the figure with an updated version (in preparation).

Let me know when you have it. For the journal of biomedical semantics my boss needs to approve the paper as well so you have time for the peer review one.

Attached please find updated version. We fixed SPARQL query to show definitions of the CDS track.

Would this sentence work?
"This encoding means there is no need to know the length of the sequence to compare positions on the different strands on a linear chromosome or genome.”

I think this is fine.

We may still need to discuss what is the best way to represent features overlap the chromosome's origin of replication with FALDO if genome database developer wants to represent the length of the features too.

Cheers,

Toshiaki

2014/01/30 22:32、Jerven Bolleman <m...@jerven.eu> のメール：