BioPAX Media Type

[Igo R]

Hi all (att: BioPAX editors),

We've got a technical question, request from Wikipathways team (Anders R.). See below.

Do you mind if we'd register a new BioPAX type (application/vnd.*) at IANA? 

We'd better apply as BioPAX.org.

Currently, as you may know, the closest existing MIME for BioPAX is probably "application/rdf+xml" 

("text/plain" response content-type is also used by, e.g., Pathway Commons), 

but for some web app/clients, it does not allow to specifically "negotiate" and get  

a BioPAX response (using content negotiation).

Shall we (seems definitely yes, good to have, in my opinion)?

If yes, which of the following do you think:

• "application/vnd.biopax+xml" (Wikipathways originally suggested)
  
• "application/vnd.biopax.rdf+xml"
  
• "application/vnd.biopax3.rdf+xml" and "application/vnd.biopax2.rdf+xml" (level-specific)
• something else (please explain)?

Regards,

[Anders Riutta @ Gladstone]

Thanks, Igor! Any one of those options sounds reasonable to me.

Anders Riutta

WikiPathways/Gladstone Institutes

[Igo R]

I would go for "application/vnd.biopax.rdf+xml"

On Wednesday, February 11, 2015 at 1:49:45 PM UTC-5, Anders Riutta @ Gladstone wrote:

Thanks, Igor! Any one of those options sounds reasonable to me.

Anders Riutta

WikiPathways/Gladstone Institutes

...

[Gary Bader]

Hi Anders - do you need to differentiate between BioPAX levels at the negotiation phase? E.g. level3 vs. potential level4 in the future?

Gary

> --
> You received this message because you are subscribed to the Google Groups "BioPAX discussion group" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to biopax-discus...@googlegroups.com.
> Visit this group at http://groups.google.com/group/biopax-discuss.
> To view this discussion on the web visit https://groups.google.com/d/msgid/biopax-discuss/ce82b449-c192-4d86-a404-b703efe6db8e%40googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.

http://baderlab.org
The Donnelly Centre - http://www.thedonnellycentre.utoronto.ca/
University of Toronto

[Anders Riutta]

Hi Gary,

Yes, that would be useful. I've seen two options for this.

1) Put the version in the media type. Drawback: need to register with IANA for every new BioPAX version.
vnd.biopax3.rdf+xml
vnd.biopax4.rdf+xml

2) Specify a version in the Accept header. Drawback: this is perfectly valid, but some HTTP clients don't support it.
vnd.biopax.rdf+xml; version=3
vnd.biopax.rdf+xml; version=4

Github uses the first option, but they don't register their media types with IANA: https://developer.github.com/v3/media/

Anders

> You received this message because you are subscribed to a topic in the Google

> Groups "BioPAX discussion group" group.

> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/biopax-discuss/L0JpNGurRm8/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to

> biopax-discus...@googlegroups.com.
> Visit this group at http://groups.google.com/group/biopax-discuss.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/biopax-discuss/C3AC55BD-239B-4F22-937C-E0644BF304E4%40utoronto.ca.

[Igo R]

I think, such fine-tuning is not required, and just "vnd.biopax.rdf+xml " is ok,

because a) one can tell L2 from L3 by looking in the RDF header (and e.g. Paxtools does not have to know in advance which level it is); b) BioPAX L2 better not use anymore 

(it's easy to convert to Level3 with Paxtools, lossless) ;)

On Thursday, February 12, 2015 at 3:06:54 PM UTC-5, Anders Riutta @ Gladstone wrote:

Hi Gary,

Yes, that would be useful. I've seen two options for this.

1) Put the version in the media type. Drawback: need to register with IANA for every new BioPAX version.
vnd.biopax3.rdf+xml
vnd.biopax4.rdf+xml

2) Specify a version in the Accept header. Drawback: this is perfectly valid, but some HTTP clients don't support it.
vnd.biopax.rdf+xml; version=3
vnd.biopax.rdf+xml; version=4

Github uses the first option, but they don't register their media types with IANA: https://developer.github.com/v3/media/

Anders

...

[Igo R]

I think, "application/vnd.biopax.rdf+xml" would be good enought...

Anyway, please vote by this Sunday, 1 March 2015 23:59 PM.

Best regards,

Igor R.

UofT

On Thursday, February 12, 2015 at 3:12:18 PM UTC-5, Igo R wrote:

I think, such fine-tuning is not required, and just "vnd.biopax.rdf+xml " is ok,

because a) one can tell L2 from L3 by looking in the RDF header (and e.g. Paxtools does not have to know in advance which level it is); b) BioPAX L2 better not use anymore 

(it's easy to convert to Level3 with Paxtools, lossless) ;)

On Thursday, February 12, 2015 at 3:06:54 PM UTC-5, Anders Riutta @ Gladstone wrote:

Hi Gary,

Yes, that would be useful. I've seen two options for this.

1) Put the version in the media type. Drawback: need to register with IANA for every new BioPAX version.
vnd.biopax3.rdf+xml
vnd.biopax4.rdf+xml

2) Specify a version in the Accept header. Drawback: this is perfectly valid, but some HTTP clients don't support it.
vnd.biopax.rdf+xml; version=3
vnd.biopax.rdf+xml; version=4

Github uses the first option, but they don't register their media types with IANA: https://developer.github.com/v3/media/

Anders

...

[Igo R]

Ok, we'll apply for "application/vnd.biopax.rdf+xml".

[Igo R]

IANA has registered the following media type with me as a point of contact:

Application/Vendor Tree - vnd.biopax.rdf+xml

Please see:

http://www.iana.org/assignments/media-types (and here).

If we need to update the contact information, we are to send a message to iana@iana.org.

(I got the confirmation email from Amanda Baber, IANA Senior Specialist, ICANN, on 10 June 2015.)