API -access

28 views
Skip to first unread message

Deepa Maheshvare

unread,
Nov 28, 2017, 10:17:17 AM11/28/17
to SABIO-RK
Hello Everyone,
I am trying to use the rest API to access the entries pertaining to a EC number.
When I use "EnzymeType":"wildtype", HTTP:Error 404 appears.However,setting the same query options manually on the webpage displays results.When I exclude the "EnzymeType":"wildtype" from the query dictionary the code gives output.Adding "EnzymeType":"wildtype"  causes the error.

I would be grateful for any help you could offer.
I am also attaching the python file for your kind consideration.

Thanks Deepa
SABIO_rest.py

Matthias König

unread,
Nov 29, 2017, 5:06:04 AM11/29/17
to SABIO-RK
As far as I can remember that is an issue with the webservice.
I reported this some time ago, i.e. "filtering by wildtype is not possible via web services"
I wrote a summary of the issues I found in the following document
with the wildtype filtering being one of the issues.

Many of the things listed there have already been fixed, but I think the wildtype filtering is currently not possible (but would be very important for the usability of the web services).

Deepa Maheshvare

unread,
Nov 29, 2017, 7:24:26 AM11/29/17
to SABIO-RK


Hi Matthias,
Thanks a lot for the response.I hope the wildtype filtering issue gets fixed soon.


Deepa Maheshvare

unread,
Nov 29, 2017, 7:27:21 AM11/29/17
to SABIO-RK
Hi All,
Could someone give some advice on how to obtain the output in xml format?

Deepa

PS:I am using the code attached to get the output in xls format
SABIO_rest.py

Ulrike Wittig

unread,
Dec 1, 2017, 5:01:10 AM12/1/17
to SABIO-RK
Hi Deepa,
sorry, but currently XML export is only available for lists of suggestions as you can find in the web services documentation: http://sabiork.h-its.org/layouts/content/docuRESTfulWeb/RESTWebserviceIntro.gsp

Best regards,
Ulrike

Ulrike Wittig

unread,
Dec 1, 2017, 5:03:55 AM12/1/17
to SABIO-RK
Hi Deepa, hi Matthias,

we are working on it and will fix the problem.

Best regards,
Ulrike

Deepa Maheshvare

unread,
Dec 5, 2017, 2:17:19 AM12/5/17
to SABIO-RK
Hi Ulrike,
Could you please provide a sample python script for XML export for lists of suggestions?

Many thanks,
Deepa

Deepa Maheshvare

unread,
Dec 5, 2017, 2:29:45 AM12/5/17
to SABIO-RK
I wish to query information about the protein complex provided for Modifier-Catalyst of an entry.



I tried adding 'Modifers'(also Catalyst)in the query dic,in the sample code provided here .But the query failed.

query = {'format':'tsv', 'fields[]':['EntryID', 'Organism', 'UniprotID','ECNumber', 'Parameter', 'Modifiers']}     

Could someone advice me on how to retrieve this information?

 Thanks,
Deepa


On Fri, Dec 1, 2017 at 4:01 PM, Deepa Maheshvare <deepama...@gmail.com> wrote:
Hi Ulrike,
Thanks for the response.
Would it be possible to print at least the Variant type in the output?
I wish to get information about whether the Variant is  a wildtype or a mutant.

I tried adding 'Variant' in the query dic,in the sample code provided here .

query = {'format':'tsv', 'fields[]':['EntryID', 'Organism', 'UniprotID','ECNumber', 'Parameter', 'Variant']} 

However,the variant type is not listed in the results column.

Thanks,
Deepa

--
You received this message because you are subscribed to the Google Groups "SABIO-RK" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sabio-rk+unsubscribe@googlegroups.com.
To post to this group, send email to sabi...@googlegroups.com.
Visit this group at https://groups.google.com/group/sabio-rk.
To view this discussion on the web visit https://groups.google.com/d/msgid/sabio-rk/76353ddc-fece-45eb-b135-64a9cfb3ea99%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.


Niels Zondervan

unread,
Jan 10, 2018, 10:09:54 AM1/10/18
to SABIO-RK
Hi Deepa,

I just tried to retrieve the EnzymeType data via the web API and it works. The issue has been fixed:
query = {'format':'tsv', 'fields[]':['EntryID', 'Organism', 'UniprotID','ECNumber', 'Parameter','PubMedID','EnzymeType']}

Regards,

Niels


On Tuesday, November 28, 2017 at 4:17:17 PM UTC+1, Deepa Maheshvare wrote:
Reply all
Reply to author
Forward
0 new messages