[Obo-anatomy] Best practice for citing manuscripts with DOIs etc

[Chris Mungall]

Sofia is developing a planaria ontology and often requires citing works
like

Hallez, P. (1887). Embryogénie des Dendrocoeles d’eau douce, Vol 16.
4)
Ijima, I. (1884). Untersuchungeniiber den Bau und die
Entwicklungsgeschichte der stisswasser-Dendrocoelen(Tricladen). Vol Bd.
40.
Le Moigne, A. (1963). Etude du developpement embryonnaire de Polycelis
nigra (Turbellarie - Triclade). Bulletin de la Societe Zoologique de
France 88, 403-422.
Metschnikoff, E. (1883). Die embryologie von Planaria polychroa.
Zeitschrift fur wissenschaftliche Zoologie 38, 331-354.

I recommended URLs like:
http://www.biodiversitylibrary.org/item/138498#page/341/mode/1up

Other suggestions?

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[Chris Mungall]

Perfect! And we can register OCLC as a prefix as well.

On 2 Feb 2017, at 16:42, Vision, Todd J wrote:

> One option would be to search for the titles in Worldcat:
> http://www.worldcat.org/advancedsearch
> If they aren’t in BHL, there is still a reasonable chance of finding
> them there. In which case you can use Worldcat's OCLC identifier to
> form a URL:
> http://www.worldcat.org/oclc/464776945
>
> cheers,
> Todd
>
>> On Feb 2, 2017, at 6:51 PM, Robb, Sofia <s...@stowers.org> wrote:
>>
>> Yeah! You found a url for one of my articles! What do I do with the
>> rest that I cannot find urls for?
>>
>> —
>> Sofia M.C. Robb, Ph.D
>> Genomic Scientist
>> Stowers Institute for Medical Research
>> s...@stowers.org

>>
>>
>> On 2/2/17, 4:48 PM, "Chris Mungall" <cjmu...@lbl.gov> wrote:
>>
>>> Sofia is developing a planaria ontology and often requires citing
>>> works
>>> like
>>>
>>> Hallez, P. (1887). Embryogénie des Dendrocoeles d’eau douce, Vol
>>> 16.
>>> 4)
>>> Ijima, I. (1884). Untersuchungeniiber den Bau und die
>>> Entwicklungsgeschichte der stisswasser-Dendrocoelen(Tricladen). Vol
>>> Bd.
>>> 40.
>>> Le Moigne, A. (1963). Etude du developpement embryonnaire de
>>> Polycelis
>>> nigra (Turbellarie - Triclade). Bulletin de la Societe Zoologique de
>>> France 88, 403-422.
>>> Metschnikoff, E. (1883). Die embryologie von Planaria polychroa.
>>> Zeitschrift fur wissenschaftliche Zoologie 38, 331-354.
>>>
>>> I recommended URLs like:
>>> http://www.biodiversitylibrary.org/item/138498#page/341/mode/1up
>>>
>>> Other suggestions?
>
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[Robb, Sofia]

I had the same hope. I still have about 5 or so after searching worldcat, biodiveristylibrary, and oclc. Many of my citations are foreign and from the 1800s. I also have one thesis from the university of Barcelona. Is there not a way to include the citation as the dbxref?

Sent from my iPhone

> On Feb 2, 2017, at 5:42 PM, Vision, Todd J <t...@bio.unc.edu> wrote:
>
> One option would be to search for the titles in Worldcat: http://www.worldcat.org/advancedsearch
> If they aren’t in BHL, there is still a reasonable chance of finding them there. In which case you can use Worldcat's OCLC identifier to form a URL:
> http://www.worldcat.org/oclc/464776945
>
> cheers,
> Todd
>
>> On Feb 2, 2017, at 6:51 PM, Robb, Sofia <s...@stowers.org> wrote:
>>
>> Yeah! You found a url for one of my articles! What do I do with the rest that I cannot find urls for?
>>
>> —
>> Sofia M.C. Robb, Ph.D
>> Genomic Scientist
>> Stowers Institute for Medical Research
>> s...@stowers.org
>>
>>
>>> On 2/2/17, 4:48 PM, "Chris Mungall" <cjmu...@lbl.gov> wrote:
>>>

>>> Sofia is developing a planaria ontology and often requires citing works
>>> like
>>>

>>> Hallez, P. (1887). Embryogeěnie des Dendrocoeles d’eau douce, Vol 16.

[Robb, Sofia]

Yeah! You found a url for one of my articles! What do I do with the rest that I cannot find urls for?


—
Sofia M.C. Robb, Ph.D
Genomic Scientist
Stowers Institute for Medical Research
s...@stowers.org









On 2/2/17, 4:48 PM, "Chris Mungall" <cjmu...@lbl.gov> wrote:

[Vision, Todd J]

One option would be to search for the titles in Worldcat: http://www.worldcat.org/advancedsearch
If they aren’t in BHL, there is still a reasonable chance of finding them there. In which case you can use Worldcat's OCLC identifier to form a URL:
http://www.worldcat.org/oclc/464776945

cheers,
Todd

> On Feb 2, 2017, at 6:51 PM, Robb, Sofia <s...@stowers.org> wrote:
>

[Chris Mungall]

You could always make a file in your repo or wiki describing the
reference, preferably give an OBO purl, and point to that.

See for example the gorefs:
https://github.com/geneontology/go-site/tree/master/metadata/gorefs

Each is a markdown file with yaml metadata embedded. We use it for
meetings, mini publications etc (as we don't have many 19th C references
in GO)

>>>> Hallez, P. (1887). Embryogénie des Dendrocoeles d’eau douce, Vol

[Sofia Robb]

That will work! Do I give them a PLANA prefixed id?

[Sofia Robb]

oh, i see, maybe plana_ref:\d+

[Chris Mungall]

No option is ideal

if you go with PLANA it's hard to configure the redirects so that it discriminates classes from references.

Can you just use the full URL? Or is there a requirement to load into Chado (which expects CURIEs rather than URLs).

Are there plans for a PlanaDB with gene IDs etc? This will presumably require reference IDs, so it may be worth thinking about the bigger picture. A common pattern is local IDs like gene0000 ref00000 all prefixed with the same database prefix.

[Robb, Sofia]

I like the way GO formats theirs. I will go with PLANA_REF:000000

— 

Sofia M.C. Robb, Ph.D

Genomic Scientist

Stowers Institute for Medical Research

s...@stowers.org