[BioMart Users] BioMart Central Portal

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[BioMart Users] BioMart Central Portal

Peter Stevenson
I was looking at http://central.biomart.org/ after reading the recent paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE biomart included in there.
However I have some quibbles about how the EMAGE interface has been represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8 release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
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Re: [BioMart Users] BioMart Central Portal

Jonathan Guberman
Hello Peter,

1. EMAP anatomy ontology database is included: it is under the "Search by organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these filters and attributes from being imported into 0.8: in your configuration XML (available at http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB) there is one MainTable/key pair listed at the top of the XML:

<MainTable>EXPRESSION_TEXT_TB__EXPRESSION_TEXT_TB__main</MainTable>
<Key>OID_109_key</Key>

However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text" field="oid_108" hideDisplay="true"internalName="oid_108_filter" key="OID_108_key" legal_qualifiers="like" qualifier="like" tableConstraint="main"/>

And

<AttributeDescription default="true" displayName="Emage ID" field="accession_1037" internalName="accession_1037"key="OID_1037_key" linkoutURL="<a href="http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s">http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s" maxLength="20"tableConstraint="main"/>

Since these filters and attributes refer to keys about which no information is provided in the XML, they can not be recreated by 0.8 and are ignored.

4. and 5. BioMart 0.8 does not currently have these capabilities, but they are planned for future releases.

Sincerely,

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
TorontoOntarioCanada M5G 0A3

Tel:         647-260-7818
Toll-free: 1-866-678-6427

On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:

I was looking at http://central.biomart.org/ after reading the recent paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE biomart included in there.
However I have some quibbles about how the EMAGE interface has been represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8 release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
_______________________________________________
Users mailing list
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Re: [BioMart Users] BioMart Central Portal

Syed Haider
Peter,


On 26/09/2011 15:12, Jonathan Guberman wrote:
> Hello Peter,
>
> 1. EMAP anatomy ontology database is included: it is under the "Search by organism" tab, under vertebrates.
> 2. User-definable linking is not currently implemented in 0.8.

^^^ v0.8 is supposed to avoid this as much as possible in the favour of
implicit (under the hood) linking. Basically, the explicitly Linked
Dataset concept of v0.7 can now be perceived as attributes and filters
of all linked datasets appearing in different sections (folders) within
the first (point of entry) dataset. This also lifts the 2 dataset
linking limit of v0.7. This  (n>20) type of linking is already
implemented and functional. However, the central.biomart.org has old
(v0.7) style configurations whereby there is no such example to
demonstrate it.

Best,
Syed

> 3. There is a problem with the 0.7 configuration that prevents these filters and attributes from being imported into 0.8: in your configuration XML (available at http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB) there is one MainTable/key pair listed at the top of the XML:
>
> <MainTable>EXPRESSION_TEXT_TB__EXPRESSION_TEXT_TB__main</MainTable>
> <Key>OID_109_key</Key>
>
> However, certain attributes and filters refer to other keys. E.g.:
> <FilterDescription displayName="Experiment ID" displayType="text" field="oid_108" hideDisplay="true"internalName="oid_108_filter" key="OID_108_key" legal_qualifiers="like" qualifier="like" tableConstraint="main"/>
>
> And
>
> <AttributeDescription default="true" displayName="Emage ID" field="accession_1037" internalName="accession_1037"key="OID_1037_key" linkoutURL="<a href="http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s">http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s" maxLength="20"tableConstraint="main"/>
>
> Since these filters and attributes refer to keys about which no information is provided in the XML, they can not be recreated by 0.8 and are ignored.
>
> 4. and 5. BioMart 0.8 does not currently have these capabilities, but they are planned for future releases.
>
> Sincerely,
>
> Jonathan Guberman, PhD
> Application Programmer
>
> Ontario Institute for Cancer Research
> MaRS Centre, South Tower
> 101 College Street, Suite 800
> Toronto, Ontario, Canada M5G 0A3
>
> Tel:         647-260-7818
> Toll-free: 1-866-678-6427
> www.oicr.on.ca<http://www.oicr.on.ca>
>
> On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:
>
> I was looking at http://central.biomart.org/ after reading the recent paper in Database.
> It's nice work, looks good, and I'm obviously happy to see the EMAGE biomart included in there.
> However I have some quibbles about how the EMAGE interface has been represented on there...
> 1. The EMAP anatomy ontology database and its 2 datasets are not included.
> 2. There is no mechanism to do linked dataset queries.
> 3. EMAGE text expression annotation dataset has several groups of filters and attributes missing.
> 4. There are no default attributes pre-selected.
> 5. There is no select all/deselect all in groups of attributes.
> I don't know if some of these are technical limitations with representing a v0.7 implementation in
> v0.8? I recognise some issues from when I tried to port to a previous v0.8 release candidate. Are
> there changes at this end that I could make to help?
> Regards,
> Peter.
> --
> Peter Stevenson         | [hidden email]<mailto:[hidden email]>
> EMAP Computer Support   | http://www.emouseatlas.org/emage
> MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
> Edinburgh EH4 2XU. U.K. |
> _______________________________________________
> Users mailing list
> [hidden email]<mailto:[hidden email]>
> https://lists.biomart.org/mailman/listinfo/users
>
>
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Re: [BioMart Users] BioMart Central Portal

Peter Stevenson
In reply to this post by Jonathan Guberman
Hi Jonathan,
Thanks for the quick reply.

 > 1. EMAP anatomy ontology database is included: it is under the "Search by organism" tab, under
vertebrates.
OK I missed that - sorry.

 > 2. User-definable linking is not currently implemented in 0.8.
This is a pity particularly for us because the EMAGE implementation relies on this feature quite
heavily.

 > 3. There is a problem with the 0.7 configuration that prevents these filters and attributes from
being imported into 0.8:
I will have to have a look at why that dataset is different to the others that have imported OK.

 > 4. and 5. BioMart 0.8 does not currently have these capabilities, but they are planned for future
releases.
Again a pity, because I think these are very useful features for users when confronted with long
lists of attributes, and also for developers to set a useful default result set.

Regards,
Peter.

On 09/26/11 15:12, Jonathan Guberman wrote:

> Hello Peter,
>
> 1. EMAP anatomy ontology database is included: it is under the "Search by organism" tab, under vertebrates.
> 2. User-definable linking is not currently implemented in 0.8.
> 3. There is a problem with the 0.7 configuration that prevents these filters and attributes from being imported into 0.8: in your configuration XML (available at http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB) there is one MainTable/key pair listed at the top of the XML:
>
> <MainTable>EXPRESSION_TEXT_TB__EXPRESSION_TEXT_TB__main</MainTable>
> <Key>OID_109_key</Key>
>
> However, certain attributes and filters refer to other keys. E.g.:
> <FilterDescription displayName="Experiment ID" displayType="text" field="oid_108" hideDisplay="true"internalName="oid_108_filter" key="OID_108_key" legal_qualifiers="like" qualifier="like" tableConstraint="main"/>
>
> And
>
> <AttributeDescription default="true" displayName="Emage ID" field="accession_1037" internalName="accession_1037"key="OID_1037_key" linkoutURL="<a href="http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s">http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s" maxLength="20"tableConstraint="main"/>
>
> Since these filters and attributes refer to keys about which no information is provided in the XML, they can not be recreated by 0.8 and are ignored.
>
> 4. and 5. BioMart 0.8 does not currently have these capabilities, but they are planned for future releases.
>
> Sincerely,
>
> Jonathan Guberman, PhD
> Application Programmer
>
> Ontario Institute for Cancer Research
> MaRS Centre, South Tower
> 101 College Street, Suite 800
> Toronto, Ontario, Canada M5G 0A3
>
> Tel:         647-260-7818
> Toll-free: 1-866-678-6427
> www.oicr.on.ca<http://www.oicr.on.ca>
>
> On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:
>
> I was looking at http://central.biomart.org/ after reading the recent paper in Database.
> It's nice work, looks good, and I'm obviously happy to see the EMAGE biomart included in there.
> However I have some quibbles about how the EMAGE interface has been represented on there...
> 1. The EMAP anatomy ontology database and its 2 datasets are not included.
> 2. There is no mechanism to do linked dataset queries.
> 3. EMAGE text expression annotation dataset has several groups of filters and attributes missing.
> 4. There are no default attributes pre-selected.
> 5. There is no select all/deselect all in groups of attributes.
> I don't know if some of these are technical limitations with representing a v0.7 implementation in
> v0.8? I recognise some issues from when I tried to port to a previous v0.8 release candidate. Are
> there changes at this end that I could make to help?
> Regards,
> Peter.
> --
> Peter Stevenson         | [hidden email]<mailto:[hidden email]>
> EMAP Computer Support   | http://www.emouseatlas.org/emage
> MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
> Edinburgh EH4 2XU. U.K. |
> _______________________________________________
> Users mailing list
> [hidden email]<mailto:[hidden email]>
> https://lists.biomart.org/mailman/listinfo/users
>
>

--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
_______________________________________________
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Re: [BioMart Users] BioMart Central Portal

Arek Kasprzyk





> 4. and 5. BioMart 0.8 does not currently have these capabilities, but they are planned for future releases.
Again a pity, because I think these are very useful features for users when confronted with long lists of attributes, and also for developers to set a useful default result set.

Regards,
Peter.



Junjun:
these features are really easy to implement. Is there a chance you could add it to the rc6 (or whatever the bmc is currently running on) for Peter please?

a






 
On 09/26/11 15:12, Jonathan Guberman wrote:
Hello Peter,

1. EMAP anatomy ontology database is included: it is under the "Search by organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these filters and attributes from being imported into 0.8: in your configuration XML (available at http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB) there is one MainTable/key pair listed at the top of the XML:

<MainTable>EXPRESSION_TEXT_TB__EXPRESSION_TEXT_TB__main</MainTable>
<Key>OID_109_key</Key>

However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text" field="oid_108" hideDisplay="true"internalName="oid_108_filter" key="OID_108_key" legal_qualifiers="like" qualifier="like" tableConstraint="main"/>

And

<AttributeDescription default="true" displayName="Emage ID" field="accession_1037" internalName="accession_1037"key="OID_1037_key" linkoutURL="<a href="http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s" target="_blank">http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s" maxLength="20"tableConstraint="main"/>

Since these filters and attributes refer to keys about which no information is provided in the XML, they can not be recreated by 0.8 and are ignored.

4. and 5. BioMart 0.8 does not currently have these capabilities, but they are planned for future releases.

Sincerely,

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:         <a href="tel:647-260-7818" value="+16472607818" target="_blank">647-260-7818
Toll-free: <a href="tel:1-866-678-6427" value="+18666786427" target="_blank">1-866-678-6427
www.oicr.on.ca<http://www.oicr.on.ca>


On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:

I was looking at http://central.biomart.org/ after reading the recent paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE biomart included in there.
However I have some quibbles about how the EMAGE interface has been represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8 release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--
Peter Stevenson         | [hidden email]<mailto:[hidden email]>

EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
_______________________________________________
Users mailing list
[hidden email]<mailto:[hidden email]>

--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
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Re: [BioMart Users] BioMart Central Portal

Junjun Zhang
Yes, this can be easily done. Ok, let's schedule that.
Junjun



From: Arek Kasprzyk <[hidden email]>
Date: Mon, 26 Sep 2011 11:15:36 -0400
To: Peter Stevenson <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal






> 4. and 5. BioMart 0.8 does not currently have these capabilities, but they are planned for future releases.
Again a pity, because I think these are very useful features for users when confronted with long lists of attributes, and also for developers to set a useful default result set.

Regards,
Peter.



Junjun:
these features are really easy to implement. Is there a chance you could add it to the rc6 (or whatever the bmc is currently running on) for Peter please?

a






 
On 09/26/11 15:12, Jonathan Guberman wrote:
Hello Peter,

1. EMAP anatomy ontology database is included: it is under the "Search by organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these filters and attributes from being imported into 0.8: in your configuration XML (available at http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB) there is one MainTable/key pair listed at the top of the XML:

<MainTable>EXPRESSION_TEXT_TB__EXPRESSION_TEXT_TB__main</MainTable>
<Key>OID_109_key</Key>

However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text" field="oid_108" hideDisplay="true"internalName="oid_108_filter" key="OID_108_key" legal_qualifiers="like" qualifier="like" tableConstraint="main"/>

And

<AttributeDescription default="true" displayName="Emage ID" field="accession_1037" internalName="accession_1037"key="OID_1037_key" linkoutURL="<a href="http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s" target="_blank">http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s" maxLength="20"tableConstraint="main"/>

Since these filters and attributes refer to keys about which no information is provided in the XML, they can not be recreated by 0.8 and are ignored.

4. and 5. BioMart 0.8 does not currently have these capabilities, but they are planned for future releases.

Sincerely,

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:         <a href="tel:647-260-7818" value="+16472607818" target="_blank">647-260-7818
Toll-free: <a href="tel:1-866-678-6427" value="+18666786427" target="_blank">1-866-678-6427
www.oicr.on.ca<http://www.oicr.on.ca>


On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:

I was looking at http://central.biomart.org/ after reading the recent paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE biomart included in there.
However I have some quibbles about how the EMAGE interface has been represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8 release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--
Peter Stevenson         | [hidden email]<mailto:[hidden email]>

EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
_______________________________________________
Users mailing list
[hidden email]<mailto:[hidden email]>

--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
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Re: [BioMart Users] BioMart Central Portal

Arek Kasprzyk
In reply to this post by Peter Stevenson



> 2. User-definable linking is not currently implemented in 0.8.
This is a pity particularly for us because the EMAGE implementation relies on this feature quite heavily.


Hi Peter,
it would be helpful if could suggest what type of linking you are after. This can be pre-configured for you on BMC so your users would not be affected. In the future we'll be able to do add your source yourself and configure it in the Central Registry  through our configuration tool MConfigurator but for now you need to do via email :)

a

 


On 09/26/11 15:12, Jonathan Guberman wrote:
Hello Peter,

1. EMAP anatomy ontology database is included: it is under the "Search by organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these filters and attributes from being imported into 0.8: in your configuration XML (available at http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB) there is one MainTable/key pair listed at the top of the XML:

<MainTable>EXPRESSION_TEXT_TB__EXPRESSION_TEXT_TB__main</MainTable>
<Key>OID_109_key</Key>

However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text" field="oid_108" hideDisplay="true"internalName="oid_108_filter" key="OID_108_key" legal_qualifiers="like" qualifier="like" tableConstraint="main"/>

And

<AttributeDescription default="true" displayName="Emage ID" field="accession_1037" internalName="accession_1037"key="OID_1037_key" linkoutURL="<a href="http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s" target="_blank">http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s" maxLength="20"tableConstraint="main"/>

Since these filters and attributes refer to keys about which no information is provided in the XML, they can not be recreated by 0.8 and are ignored.

4. and 5. BioMart 0.8 does not currently have these capabilities, but they are planned for future releases.

Sincerely,

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:         <a href="tel:647-260-7818" value="+16472607818" target="_blank">647-260-7818
Toll-free: <a href="tel:1-866-678-6427" value="+18666786427" target="_blank">1-866-678-6427
www.oicr.on.ca<http://www.oicr.on.ca>


On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:

I was looking at http://central.biomart.org/ after reading the recent paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE biomart included in there.
However I have some quibbles about how the EMAGE interface has been represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8 release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--
Peter Stevenson         | [hidden email]<mailto:[hidden email]>

EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
_______________________________________________
Users mailing list
[hidden email]<mailto:[hidden email]>

--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
_______________________________________________
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Re: [BioMart Users] BioMart Central Portal

Peter Stevenson
Hi Arek,
I just meant linking in the v0.7 sense of using importables/exportables in order for the user to get
attributes from separate datasets. I can give details of the importables/exportables I used if
that's useful. However it sounds from the replies from Jonathan and Syed that its possibly not that
straightforward to bring that type of configuration into a v0.8 model?
Regards,
Peter.

On 09/26/11 19:14, Arek Kasprzyk wrote:

>>
>>
>>> 2. User-definable linking is not currently implemented in 0.8.
>> This is a pity particularly for us because the EMAGE implementation relies
>> on this feature quite heavily.
>>
>>
> Hi Peter,
> it would be helpful if could suggest what type of linking you are after.
> This can be pre-configured for you on BMC so your users would not be
> affected. In the future we'll be able to do add your source yourself and
> configure it in the Central Registry  through our configuration tool
> MConfigurator but for now you need to do via email :)
>
> a
>
>
>
>>
>>
>> On 09/26/11 15:12, Jonathan Guberman wrote:
>>
>>> Hello Peter,
>>>
>>> 1. EMAP anatomy ontology database is included: it is under the "Search by
>>> organism" tab, under vertebrates.
>>> 2. User-definable linking is not currently implemented in 0.8.
>>> 3. There is a problem with the 0.7 configuration that prevents these
>>> filters and attributes from being imported into 0.8: in your configuration
>>> XML (available at http://biomart.emouseatlas.**
>>> org/biomart/martservice?type=**configuration&dataset=**EXPRESSION_TEXT_TB<http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB>)
>>> there is one MainTable/key pair listed at the top of the XML:
>>>
>>> <MainTable>EXPRESSION_TEXT_TB_**_EXPRESSION_TEXT_TB__main</**MainTable>
>>> <Key>OID_109_key</Key>
>>>
>>> However, certain attributes and filters refer to other keys. E.g.:
>>> <FilterDescription displayName="Experiment ID" displayType="text"
>>> field="oid_108" hideDisplay="true"**internalName="oid_108_filter"
>>> key="OID_108_key" legal_qualifiers="like" qualifier="like"
>>> tableConstraint="main"/>
>>>
>>> And
>>>
>>> <AttributeDescription default="true" displayName="Emage ID"
>>> field="accession_1037" internalName="accession_1037"**key="OID_1037_key"
>>> linkoutURL="http://www.**emouseatlas.org/emagewebapp/**
>>> pages/emage_entry_page.jsf?id=**EMAGE:%s" maxLength="20"tableConstraint=*
>>> *"main"/>
>>>
>>> Since these filters and attributes refer to keys about which no
>>> information is provided in the XML, they can not be recreated by 0.8 and are
>>> ignored.
>>>
>>> 4. and 5. BioMart 0.8 does not currently have these capabilities, but they
>>> are planned for future releases.
>>>
>>> Sincerely,
>>>
>>> Jonathan Guberman, PhD
>>> Application Programmer
>>>
>>> Ontario Institute for Cancer Research
>>> MaRS Centre, South Tower
>>> 101 College Street, Suite 800
>>> Toronto, Ontario, Canada M5G 0A3
>>>
>>> Tel:         647-260-7818
>>> Toll-free: 1-866-678-6427
>>> www.oicr.on.ca<http://www.**oicr.on.ca<http://www.oicr.on.ca>>
>>>
>>>
>>> On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:
>>>
>>> I was looking at http://central.biomart.org/ after reading the recent
>>> paper in Database.
>>> It's nice work, looks good, and I'm obviously happy to see the EMAGE
>>> biomart included in there.
>>> However I have some quibbles about how the EMAGE interface has been
>>> represented on there...
>>> 1. The EMAP anatomy ontology database and its 2 datasets are not included.
>>> 2. There is no mechanism to do linked dataset queries.
>>> 3. EMAGE text expression annotation dataset has several groups of filters
>>> and attributes missing.
>>> 4. There are no default attributes pre-selected.
>>> 5. There is no select all/deselect all in groups of attributes.
>>> I don't know if some of these are technical limitations with representing
>>> a v0.7 implementation in
>>> v0.8? I recognise some issues from when I tried to port to a previous v0.8
>>> release candidate. Are
>>> there changes at this end that I could make to help?
>>> Regards,
>>> Peter.
>>> --
>>> Peter Stevenson         | [hidden email]<**mailto:
>>> Peter.Stevenson@hgu.**mrc.ac.uk<[hidden email]>>
>>>
>>> EMAP Computer Support   | http://www.emouseatlas.org/**emage<http://www.emouseatlas.org/emage>
>>> MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
>>> Edinburgh EH4 2XU. U.K. |
>>> ______________________________**_________________
>>> Users mailing list
>>> [hidden email]<mailto:Users**@biomart.org<[hidden email]>>
>>>
>>> https://lists.biomart.org/**mailman/listinfo/users<https://lists.biomart.org/mailman/listinfo/users>
>>>
>>>
>>>
>> --
>> Peter Stevenson         | [hidden email]
>> EMAP Computer Support   | http://www.emouseatlas.org/**emage<http://www.emouseatlas.org/emage>
>> MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
>> Edinburgh EH4 2XU. U.K. |
>> ______________________________**_________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/**mailman/listinfo/users<https://lists.biomart.org/mailman/listinfo/users>
>>
>

--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
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Re: [BioMart Users] BioMart Central Portal

Arek Kasprzyk
Hi Peter,
i did not make myself clear. I was not talking about bringing user defined linking back in. I was more thinking along the lines that there are typically certain datasets and that your users should like to link in order to do their favourite multi-dataset queries. If you tell us what they are we'll be able to preconfigure the interface such that these queries become possible again without users being forced to do the GUI gymnastics as they used to do in 0.7.

We just need concrete examples of  multi-datasets queries that your users typically do and we could preconfigure them for you if it makes sense.

As i mentioned in my previoius email, in the future you will be able to do such things on the central portal yourself but this is ... in the future.

For now we need an email from you with concrete examples so we can see if we can help you and keep your users happy :)

a





On Tue, Sep 27, 2011 at 9:01 AM, Peter Stevenson <[hidden email]> wrote:
Hi Arek,
I just meant linking in the v0.7 sense of using importables/exportables in order for the user to get attributes from separate datasets. I can give details of the importables/exportables I used if that's useful. However it sounds from the replies from Jonathan and Syed that its possibly not that straightforward to bring that type of configuration into a v0.8 model?
Regards,
Peter.


On 09/26/11 19:14, Arek Kasprzyk wrote:


2. User-definable linking is not currently implemented in 0.8.
This is a pity particularly for us because the EMAGE implementation relies
on this feature quite heavily.


Hi Peter,
it would be helpful if could suggest what type of linking you are after.
This can be pre-configured for you on BMC so your users would not be
affected. In the future we'll be able to do add your source yourself and
configure it in the Central Registry  through our configuration tool
MConfigurator but for now you need to do via email :)

a





On 09/26/11 15:12, Jonathan Guberman wrote:

Hello Peter,

1. EMAP anatomy ontology database is included: it is under the "Search by
organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these
filters and attributes from being imported into 0.8: in your configuration
XML (available at http://biomart.emouseatlas.**
org/biomart/martservice?type=**configuration&dataset=**EXPRESSION_TEXT_TB<http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB>)

there is one MainTable/key pair listed at the top of the XML:

<MainTable>EXPRESSION_TEXT_TB_**_EXPRESSION_TEXT_TB__main</**MainTable>
<Key>OID_109_key</Key>

However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text"
field="oid_108" hideDisplay="true"**internalName="oid_108_filter"
key="OID_108_key" legal_qualifiers="like" qualifier="like"
tableConstraint="main"/>

And

<AttributeDescription default="true" displayName="Emage ID"
field="accession_1037" internalName="accession_1037"**key="OID_1037_key"
linkoutURL="http://www.**emouseatlas.org/emagewebapp/**
pages/emage_entry_page.jsf?id=**EMAGE:%s" maxLength="20"tableConstraint=*
*"main"/>

Since these filters and attributes refer to keys about which no
information is provided in the XML, they can not be recreated by 0.8 and are
ignored.

4. and 5. BioMart 0.8 does not currently have these capabilities, but they
are planned for future releases.

Sincerely,

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:         <a href="tel:647-260-7818" value="+16472607818" target="_blank">647-260-7818
Toll-free: <a href="tel:1-866-678-6427" value="+18666786427" target="_blank">1-866-678-6427
www.oicr.on.ca<http://www.**oicr.on.ca<http://www.oicr.on.ca>>



On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:

I was looking at http://central.biomart.org/ after reading the recent
paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE
biomart included in there.
However I have some quibbles about how the EMAGE interface has been
represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters
and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing
a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8
release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--
Peter Stevenson         | [hidden email]<**mailto:
Peter.Stevenson@hgu.**mrc.ac.uk<[hidden email]>>

EMAP Computer Support   | http://www.emouseatlas.org/**emage<http://www.emouseatlas.org/emage>

MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
______________________________**_________________
Users mailing list
[hidden email]<mailto:[hidden email]**@biomart.org<[hidden email]>>

https://lists.biomart.org/**mailman/listinfo/users<https://lists.biomart.org/mailman/listinfo/users>



--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/**emage<http://www.emouseatlas.org/emage>

MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
______________________________**_________________
Users mailing list
[hidden email]
https://lists.biomart.org/**mailman/listinfo/users<https://lists.biomart.org/mailman/listinfo/users>



--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |


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Re: [BioMart Users] BioMart Central Portal

Peter Stevenson
Hi Arek,
Thank you for your offer of help.
Here are some examples, and if you can do something with them that would be great:-

EMAGE text expression annotation dataset has attribute "Atlas ontology ID of tissue (text annotation) " ie the ID of the anatomy ontology component that has been annotated, but users would like to know the component name, component path, developmental stage
and so on for that ID. These attributes are in the dataset Anatomy components (component details), where the common attribute is ID (timed stages).

From the datasets Anatomy components (component details), and Anatomy components (including subcomponents), users would like to know if the anatomy components they are interested in have gene expression annotated in EMAGE. Details of the annotation (gene, strength, pattern etc) are in the EMAGE text expression annotation dataset. As above, the common attribute is the ontology ID.

The EMAGE submission dataset contains data regarding an individual assay submitted to EMAGE. However it does not have details of the detection reagents (probes) used, these details are in the EMAGE experiment dataset. Users would be interested in the probe details for EMAGE submissions that they have found. There are several common attributes between these datasets but the most obvious one would be the EMAGE ID.
In the other direction, users might search for probes in the EMAGE experiment dataset and want to know more details about the EMAGE submission.

The EMAGE submission dataset does not have details of spatial expression annotation, this is in the EMAGE spatial expression dataset. It is likely that users would want to know if a submission they had found has spatial expression annotated.
In the other direction, users looking for spatial expression might want to know more details about the submission. The EMAGE ID would be the common attribute again here.

I hope that this makes sense but obviously let me know if you need more information.

Regards,
Peter.

On 27/09/2011 15:38, Arek Kasprzyk wrote:
Hi Peter,
i did not make myself clear. I was not talking about bringing user defined linking back in. I was more thinking along the lines that there are typically certain datasets and that your users should like to link in order to do their favourite multi-dataset queries. If you tell us what they are we'll be able to preconfigure the interface such that these queries become possible again without users being forced to do the GUI gymnastics as they used to do in 0.7.

We just need concrete examples of  multi-datasets queries that your users typically do and we could preconfigure them for you if it makes sense.

As i mentioned in my previoius email, in the future you will be able to do such things on the central portal yourself but this is ... in the future.

For now we need an email from you with concrete examples so we can see if we can help you and keep your users happy :)

a





On Tue, Sep 27, 2011 at 9:01 AM, Peter Stevenson <[hidden email]> wrote:
Hi Arek,
I just meant linking in the v0.7 sense of using importables/exportables in order for the user to get attributes from separate datasets. I can give details of the importables/exportables I used if that's useful. However it sounds from the replies from Jonathan and Syed that its possibly not that straightforward to bring that type of configuration into a v0.8 model?
Regards,
Peter.


On 09/26/11 19:14, Arek Kasprzyk wrote:


2. User-definable linking is not currently implemented in 0.8.
This is a pity particularly for us because the EMAGE implementation relies
on this feature quite heavily.


Hi Peter,
it would be helpful if could suggest what type of linking you are after.
This can be pre-configured for you on BMC so your users would not be
affected. In the future we'll be able to do add your source yourself and
configure it in the Central Registry  through our configuration tool
MConfigurator but for now you need to do via email :)

a





On 09/26/11 15:12, Jonathan Guberman wrote:

Hello Peter,

1. EMAP anatomy ontology database is included: it is under the "Search by
organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these
filters and attributes from being imported into 0.8: in your configuration
XML (available at http://biomart.emouseatlas.**
org/biomart/martservice?type=**configuration&dataset=**EXPRESSION_TEXT_TB<http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB>)

there is one MainTable/key pair listed at the top of the XML:

<MainTable>EXPRESSION_TEXT_TB_**_EXPRESSION_TEXT_TB__main</**MainTable>
<Key>OID_109_key</Key>

However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text"
field="oid_108" hideDisplay="true"**internalName="oid_108_filter"
key="OID_108_key" legal_qualifiers="like" qualifier="like"
tableConstraint="main"/>

And

<AttributeDescription default="true" displayName="Emage ID"
field="accession_1037" internalName="accession_1037"**key="OID_1037_key"
linkoutURL="http://www.**emouseatlas.org/emagewebapp/**
pages/emage_entry_page.jsf?id=**EMAGE:%s" maxLength="20"tableConstraint=*
*"main"/>

Since these filters and attributes refer to keys about which no
information is provided in the XML, they can not be recreated by 0.8 and are
ignored.

4. and 5. BioMart 0.8 does not currently have these capabilities, but they
are planned for future releases.

Sincerely,

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:         <a moz-do-not-send="true" href="tel:647-260-7818" value="+16472607818" target="_blank">647-260-7818
Toll-free: <a moz-do-not-send="true" href="tel:1-866-678-6427" value="+18666786427" target="_blank">1-866-678-6427
www.oicr.on.ca<http://www.**oicr.on.ca<http://www.oicr.on.ca>>



On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:

I was looking at http://central.biomart.org/ after reading the recent
paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE
biomart included in there.
However I have some quibbles about how the EMAGE interface has been
represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters
and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing
a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8
release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--


--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a moz-do-not-send="true" href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |



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Re: [BioMart Users] BioMart Central Portal

Arek Kasprzyk
Hi Junjun,
would it be difficult for you to re-configure this for Peter accordingly?

a

On Wed, Sep 28, 2011 at 6:13 AM, peters <[hidden email]> wrote:
Hi Arek,
Thank you for your offer of help.
Here are some examples, and if you can do something with them that would be great:-

EMAGE text expression annotation dataset has attribute "Atlas ontology ID of tissue (text annotation) " ie the ID of the anatomy ontology component that has been annotated, but users would like to know the component name, component path, developmental stage
and so on for that ID. These attributes are in the dataset Anatomy components (component details), where the common attribute is ID (timed stages).

From the datasets Anatomy components (component details), and Anatomy components (including subcomponents), users would like to know if the anatomy components they are interested in have gene expression annotated in EMAGE. Details of the annotation (gene, strength, pattern etc) are in the EMAGE text expression annotation dataset. As above, the common attribute is the ontology ID.

The EMAGE submission dataset contains data regarding an individual assay submitted to EMAGE. However it does not have details of the detection reagents (probes) used, these details are in the EMAGE experiment dataset. Users would be interested in the probe details for EMAGE submissions that they have found. There are several common attributes between these datasets but the most obvious one would be the EMAGE ID.
In the other direction, users might search for probes in the EMAGE experiment dataset and want to know more details about the EMAGE submission.

The EMAGE submission dataset does not have details of spatial expression annotation, this is in the EMAGE spatial expression dataset. It is likely that users would want to know if a submission they had found has spatial expression annotated.
In the other direction, users looking for spatial expression might want to know more details about the submission. The EMAGE ID would be the common attribute again here.

I hope that this makes sense but obviously let me know if you need more information.

Regards,
Peter.


On 27/09/2011 15:38, Arek Kasprzyk wrote:
Hi Peter,
i did not make myself clear. I was not talking about bringing user defined linking back in. I was more thinking along the lines that there are typically certain datasets and that your users should like to link in order to do their favourite multi-dataset queries. If you tell us what they are we'll be able to preconfigure the interface such that these queries become possible again without users being forced to do the GUI gymnastics as they used to do in 0.7.

We just need concrete examples of  multi-datasets queries that your users typically do and we could preconfigure them for you if it makes sense.

As i mentioned in my previoius email, in the future you will be able to do such things on the central portal yourself but this is ... in the future.

For now we need an email from you with concrete examples so we can see if we can help you and keep your users happy :)

a





On Tue, Sep 27, 2011 at 9:01 AM, Peter Stevenson <[hidden email]> wrote:
Hi Arek,
I just meant linking in the v0.7 sense of using importables/exportables in order for the user to get attributes from separate datasets. I can give details of the importables/exportables I used if that's useful. However it sounds from the replies from Jonathan and Syed that its possibly not that straightforward to bring that type of configuration into a v0.8 model?
Regards,
Peter.


On 09/26/11 19:14, Arek Kasprzyk wrote:


2. User-definable linking is not currently implemented in 0.8.
This is a pity particularly for us because the EMAGE implementation relies
on this feature quite heavily.


Hi Peter,
it would be helpful if could suggest what type of linking you are after.
This can be pre-configured for you on BMC so your users would not be
affected. In the future we'll be able to do add your source yourself and
configure it in the Central Registry  through our configuration tool
MConfigurator but for now you need to do via email :)

a





On 09/26/11 15:12, Jonathan Guberman wrote:

Hello Peter,

1. EMAP anatomy ontology database is included: it is under the "Search by
organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these
filters and attributes from being imported into 0.8: in your configuration
XML (available at http://biomart.emouseatlas.**
org/biomart/martservice?type=**configuration&dataset=**EXPRESSION_TEXT_TB<http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB>)

there is one MainTable/key pair listed at the top of the XML:

<MainTable>EXPRESSION_TEXT_TB_**_EXPRESSION_TEXT_TB__main</**MainTable>
<Key>OID_109_key</Key>

However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text"
field="oid_108" hideDisplay="true"**internalName="oid_108_filter"
key="OID_108_key" legal_qualifiers="like" qualifier="like"
tableConstraint="main"/>

And

<AttributeDescription default="true" displayName="Emage ID"
field="accession_1037" internalName="accession_1037"**key="OID_1037_key"
linkoutURL="http://www.**emouseatlas.org/emagewebapp/**
pages/emage_entry_page.jsf?id=**EMAGE:%s" maxLength="20"tableConstraint=*
*"main"/>

Since these filters and attributes refer to keys about which no
information is provided in the XML, they can not be recreated by 0.8 and are
ignored.

4. and 5. BioMart 0.8 does not currently have these capabilities, but they
are planned for future releases.

Sincerely,

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:         <a href="tel:647-260-7818" value="+16472607818" target="_blank">647-260-7818
Toll-free: <a href="tel:1-866-678-6427" value="+18666786427" target="_blank">1-866-678-6427
www.oicr.on.ca<http://www.**oicr.on.ca<http://www.oicr.on.ca>>



On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:

I was looking at http://central.biomart.org/ after reading the recent
paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE
biomart included in there.
However I have some quibbles about how the EMAGE interface has been
represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters
and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing
a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8
release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--


--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |




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https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] BioMart Central Portal

Junjun Zhang
Looks like we just need to create a bunch of pointer attributes and ensure link is added properly. We will test it out first to see if it works as expected.
Junjun
Sent from my BBerry

 
From: Arek Kasprzyk [mailto:[hidden email]]
Sent: Wednesday, September 28, 2011 08:29 AM
To: peters <[hidden email]>
Cc: [hidden email] <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal
 
Hi Junjun,
would it be difficult for you to re-configure this for Peter accordingly?

a

On Wed, Sep 28, 2011 at 6:13 AM, peters <[hidden email]> wrote:
Hi Arek,
Thank you for your offer of help.
Here are some examples, and if you can do something with them that would be great:-

EMAGE text expression annotation dataset has attribute "Atlas ontology ID of tissue (text annotation) " ie the ID of the anatomy ontology component that has been annotated, but users would like to know the component name, component path, developmental stage
and so on for that ID. These attributes are in the dataset Anatomy components (component details), where the common attribute is ID (timed stages).

From the datasets Anatomy components (component details), and Anatomy components (including subcomponents), users would like to know if the anatomy components they are interested in have gene expression annotated in EMAGE. Details of the annotation (gene, strength, pattern etc) are in the EMAGE text expression annotation dataset. As above, the common attribute is the ontology ID.

The EMAGE submission dataset contains data regarding an individual assay submitted to EMAGE. However it does not have details of the detection reagents (probes) used, these details are in the EMAGE experiment dataset. Users would be interested in the probe details for EMAGE submissions that they have found. There are several common attributes between these datasets but the most obvious one would be the EMAGE ID.
In the other direction, users might search for probes in the EMAGE experiment dataset and want to know more details about the EMAGE submission.

The EMAGE submission dataset does not have details of spatial expression annotation, this is in the EMAGE spatial expression dataset. It is likely that users would want to know if a submission they had found has spatial expression annotated.
In the other direction, users looking for spatial expression might want to know more details about the submission. The EMAGE ID would be the common attribute again here.

I hope that this makes sense but obviously let me know if you need more information.

Regards,
Peter.


On 27/09/2011 15:38, Arek Kasprzyk wrote:
Hi Peter,
i did not make myself clear. I was not talking about bringing user defined linking back in. I was more thinking along the lines that there are typically certain datasets and that your users should like to link in order to do their favourite multi-dataset queries. If you tell us what they are we'll be able to preconfigure the interface such that these queries become possible again without users being forced to do the GUI gymnastics as they used to do in 0.7.

We just need concrete examples of  multi-datasets queries that your users typically do and we could preconfigure them for you if it makes sense.

As i mentioned in my previoius email, in the future you will be able to do such things on the central portal yourself but this is ... in the future.

For now we need an email from you with concrete examples so we can see if we can help you and keep your users happy :)

a





On Tue, Sep 27, 2011 at 9:01 AM, Peter Stevenson <[hidden email]> wrote:
Hi Arek,
I just meant linking in the v0.7 sense of using importables/exportables in order for the user to get attributes from separate datasets. I can give details of the importables/exportables I used if that's useful. However it sounds from the replies from Jonathan and Syed that its possibly not that straightforward to bring that type of configuration into a v0.8 model?
Regards,
Peter.


On 09/26/11 19:14, Arek Kasprzyk wrote:


2. User-definable linking is not currently implemented in 0.8.
This is a pity particularly for us because the EMAGE implementation relies
on this feature quite heavily.


Hi Peter,
it would be helpful if could suggest what type of linking you are after.
This can be pre-configured for you on BMC so your users would not be
affected. In the future we'll be able to do add your source yourself and
configure it in the Central Registry  through our configuration tool
MConfigurator but for now you need to do via email :)

a





On 09/26/11 15:12, Jonathan Guberman wrote:

Hello Peter,

1. EMAP anatomy ontology database is included: it is under the "Search by
organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these
filters and attributes from being imported into 0.8: in your configuration
XML (available at http://biomart.emouseatlas.**
org/biomart/martservice?type=**configuration&dataset=**EXPRESSION_TEXT_TB<http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB>)

there is one MainTable/key pair listed at the top of the XML:

<MainTable>EXPRESSION_TEXT_TB_**_EXPRESSION_TEXT_TB__main</**MainTable>
<Key>OID_109_key</Key>

However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text"
field="oid_108" hideDisplay="true"**internalName="oid_108_filter"
key="OID_108_key" legal_qualifiers="like" qualifier="like"
tableConstraint="main"/>

And

<AttributeDescription default="true" displayName="Emage ID"
field="accession_1037" internalName="accession_1037"**key="OID_1037_key"
linkoutURL="http://www.**emouseatlas.org/emagewebapp/**
pages/emage_entry_page.jsf?id=**EMAGE:%s" maxLength="20"tableConstraint=*
*"main"/>

Since these filters and attributes refer to keys about which no
information is provided in the XML, they can not be recreated by 0.8 and are
ignored.

4. and 5. BioMart 0.8 does not currently have these capabilities, but they
are planned for future releases.

Sincerely,

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:         <a href="tel:647-260-7818" value="+16472607818" target="_blank">647-260-7818
Toll-free: <a href="tel:1-866-678-6427" value="+18666786427" target="_blank">1-866-678-6427
www.oicr.on.ca<http://www.**oicr.on.ca<http://www.oicr.on.ca>>



On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:

I was looking at http://central.biomart.org/ after reading the recent
paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE
biomart included in there.
However I have some quibbles about how the EMAGE interface has been
represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters
and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing
a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8
release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--


--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |




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Re: [BioMart Users] BioMart Central Portal

Elena Rivkin
In reply to this post by Peter Stevenson
Hi Peter, 

Regarding: "EMAGE text expression annotation dataset has attribute "Atlas ontology ID of tissue (text annotation) " ie the ID of the anatomy ontology component that has been annotated, but users would like to know the component name, component path, developmental stage
and so on for that ID. These attributes are in the dataset Anatomy components (component details), where the common attribute is ID (timed stages).

From the datasets Anatomy components (component details), and Anatomy components (including subcomponents), users would like to know if the anatomy components they are interested in have gene expression annotated in EMAGE. Details of the annotation (gene, strength, pattern etc) are in the EMAGE text expression annotation dataset. As above, the common attribute is the ontology ID."

--> I couldn't find the common attribute ID that you are refering to. The only common attribute that I see is the theiler stage.

"Atlas ontology ID of tissue (text annotation) " only appears in the EMAGE text expression annotation dataset
AND
ID (timed stages) only appears in the EMAP ontology datasets. 

Thank you. 

Elena Rivkin, PhD
Outreach and Training Coordinator, Informatics and Bio-computing

Ontario Institute for Cancer Research
MaRS Centre, South Tower

101 College Street, Suite 800

Toronto, Ontario, Canada M5G 0A3


Tel: 647-258-4316

Toll-free: 1-866-678-6427

www.oicr.on.ca


This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

 


From: peters <[hidden email]>
Date: Wed, 28 Sep 2011 06:13:10 -0400
To: Arek Kasprzyk <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal

Hi Arek,
Thank you for your offer of help.
Here are some examples, and if you can do something with them that would be great:-



The EMAGE submission dataset contains data regarding an individual assay submitted to EMAGE. However it does not have details of the detection reagents (probes) used, these details are in the EMAGE experiment dataset. Users would be interested in the probe details for EMAGE submissions that they have found. There are several common attributes between these datasets but the most obvious one would be the EMAGE ID.
In the other direction, users might search for probes in the EMAGE experiment dataset and want to know more details about the EMAGE submission.

The EMAGE submission dataset does not have details of spatial expression annotation, this is in the EMAGE spatial expression dataset. It is likely that users would want to know if a submission they had found has spatial expression annotated.
In the other direction, users looking for spatial expression might want to know more details about the submission. The EMAGE ID would be the common attribute again here.

I hope that this makes sense but obviously let me know if you need more information.

Regards,
Peter.

On 27/09/2011 15:38, Arek Kasprzyk wrote:
Hi Peter,
i did not make myself clear. I was not talking about bringing user defined linking back in. I was more thinking along the lines that there are typically certain datasets and that your users should like to link in order to do their favourite multi-dataset queries. If you tell us what they are we'll be able to preconfigure the interface such that these queries become possible again without users being forced to do the GUI gymnastics as they used to do in 0.7.

We just need concrete examples of  multi-datasets queries that your users typically do and we could preconfigure them for you if it makes sense.

As i mentioned in my previoius email, in the future you will be able to do such things on the central portal yourself but this is ... in the future.

For now we need an email from you with concrete examples so we can see if we can help you and keep your users happy :)

a





On Tue, Sep 27, 2011 at 9:01 AM, Peter Stevenson <[hidden email]> wrote:
Hi Arek,
I just meant linking in the v0.7 sense of using importables/exportables in order for the user to get attributes from separate datasets. I can give details of the importables/exportables I used if that's useful. However it sounds from the replies from Jonathan and Syed that its possibly not that straightforward to bring that type of configuration into a v0.8 model?
Regards,
Peter.


On 09/26/11 19:14, Arek Kasprzyk wrote:


2. User-definable linking is not currently implemented in 0.8.
This is a pity particularly for us because the EMAGE implementation relies
on this feature quite heavily.


Hi Peter,
it would be helpful if could suggest what type of linking you are after.
This can be pre-configured for you on BMC so your users would not be
affected. In the future we'll be able to do add your source yourself and
configure it in the Central Registry  through our configuration tool
MConfigurator but for now you need to do via email :)

a





On 09/26/11 15:12, Jonathan Guberman wrote:

Hello Peter,

1. EMAP anatomy ontology database is included: it is under the "Search by
organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these
filters and attributes from being imported into 0.8: in your configuration
XML (available at http://biomart.emouseatlas.**
org/biomart/martservice?type=**configuration&dataset=**EXPRESSION_TEXT_TB<http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB>)

there is one MainTable/key pair listed at the top of the XML:

<MainTable>EXPRESSION_TEXT_TB_**_EXPRESSION_TEXT_TB__main</**MainTable>
<Key>OID_109_key</Key>

However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text"
field="oid_108" hideDisplay="true"**internalName="oid_108_filter"
key="OID_108_key" legal_qualifiers="like" qualifier="like"
tableConstraint="main"/>

And

<AttributeDescription default="true" displayName="Emage ID"
field="accession_1037" internalName="accession_1037"**key="OID_1037_key"
linkoutURL="http://www.**emouseatlas.org/emagewebapp/**
pages/emage_entry_page.jsf?id=**EMAGE:%s" maxLength="20"tableConstraint=*
*"main"/>

Since these filters and attributes refer to keys about which no
information is provided in the XML, they can not be recreated by 0.8 and are
ignored.

4. and 5. BioMart 0.8 does not currently have these capabilities, but they
are planned for future releases.

Sincerely,

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:         <a moz-do-not-send="true" href="tel:647-260-7818" value="+16472607818" target="_blank">647-260-7818
Toll-free: <a moz-do-not-send="true" href="tel:1-866-678-6427" value="+18666786427" target="_blank">1-866-678-6427
www.oicr.on.ca<http://www.**oicr.on.ca<http://www.oicr.on.ca>>



On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:

I was looking at http://central.biomart.org/ after reading the recent
paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE
biomart included in there.
However I have some quibbles about how the EMAGE interface has been
represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters
and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing
a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8
release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--


--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a moz-do-not-send="true" href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
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Re: [BioMart Users] BioMart Central Portal

Peter Stevenson
Hi Elena,
The attribute has a different label in the 2 datasets but it is the same thing.
An example would be EMAP:1234.
Regards,
Peter.

On 28/09/2011 15:48, Elena Rivkin wrote:
Hi Peter, 

Regarding: "EMAGE text expression annotation dataset has attribute "Atlas ontology ID of tissue (text annotation) " ie the ID of the anatomy ontology component that has been annotated, but users would like to know the component name, component path, developmental stage
and so on for that ID. These attributes are in the dataset Anatomy components (component details), where the common attribute is ID (timed stages).

From the datasets Anatomy components (component details), and Anatomy components (including subcomponents), users would like to know if the anatomy components they are interested in have gene expression annotated in EMAGE. Details of the annotation (gene, strength, pattern etc) are in the EMAGE text expression annotation dataset. As above, the common attribute is the ontology ID."

--> I couldn't find the common attribute ID that you are refering to. The only common attribute that I see is the theiler stage.

"Atlas ontology ID of tissue (text annotation) " only appears in the EMAGE text expression annotation dataset
AND
ID (timed stages) only appears in the EMAP ontology datasets. 

Thank you. 

Elena Rivkin, PhD
Outreach and Training Coordinator, Informatics and Bio-computing

Ontario Institute for Cancer Research
MaRS Centre, South Tower

101 College Street, Suite 800

Toronto, Ontario, Canada M5G 0A3


Tel: 647-258-4316

Toll-free: 1-866-678-6427

www.oicr.on.ca


This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

 


From: peters <[hidden email]>
Date: Wed, 28 Sep 2011 06:13:10 -0400
To: Arek Kasprzyk <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal

Hi Arek,
Thank you for your offer of help.
Here are some examples, and if you can do something with them that would be great:-



The EMAGE submission dataset contains data regarding an individual assay submitted to EMAGE. However it does not have details of the detection reagents (probes) used, these details are in the EMAGE experiment dataset. Users would be interested in the probe details for EMAGE submissions that they have found. There are several common attributes between these datasets but the most obvious one would be the EMAGE ID.
In the other direction, users might search for probes in the EMAGE experiment dataset and want to know more details about the EMAGE submission.

The EMAGE submission dataset does not have details of spatial expression annotation, this is in the EMAGE spatial expression dataset. It is likely that users would want to know if a submission they had found has spatial expression annotated.
In the other direction, users looking for spatial expression might want to know more details about the submission. The EMAGE ID would be the common attribute again here.

I hope that this makes sense but obviously let me know if you need more information.

Regards,
Peter.

On 27/09/2011 15:38, Arek Kasprzyk wrote:
Hi Peter,
i did not make myself clear. I was not talking about bringing user defined linking back in. I was more thinking along the lines that there are typically certain datasets and that your users should like to link in order to do their favourite multi-dataset queries. If you tell us what they are we'll be able to preconfigure the interface such that these queries become possible again without users being forced to do the GUI gymnastics as they used to do in 0.7.

We just need concrete examples of  multi-datasets queries that your users typically do and we could preconfigure them for you if it makes sense.

As i mentioned in my previoius email, in the future you will be able to do such things on the central portal yourself but this is ... in the future.

For now we need an email from you with concrete examples so we can see if we can help you and keep your users happy :)

a





On Tue, Sep 27, 2011 at 9:01 AM, Peter Stevenson <[hidden email]> wrote:
Hi Arek,
I just meant linking in the v0.7 sense of using importables/exportables in order for the user to get attributes from separate datasets. I can give details of the importables/exportables I used if that's useful. However it sounds from the replies from Jonathan and Syed that its possibly not that straightforward to bring that type of configuration into a v0.8 model?
Regards,
Peter.


On 09/26/11 19:14, Arek Kasprzyk wrote:


2. User-definable linking is not currently implemented in 0.8.
This is a pity particularly for us because the EMAGE implementation relies
on this feature quite heavily.


Hi Peter,
it would be helpful if could suggest what type of linking you are after.
This can be pre-configured for you on BMC so your users would not be
affected. In the future we'll be able to do add your source yourself and
configure it in the Central Registry  through our configuration tool
MConfigurator but for now you need to do via email :)

a





On 09/26/11 15:12, Jonathan Guberman wrote:

Hello Peter,

1. EMAP anatomy ontology database is included: it is under the "Search by
organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these
filters and attributes from being imported into 0.8: in your configuration
XML (available at http://biomart.emouseatlas.**
org/biomart/martservice?type=**configuration&dataset=**EXPRESSION_TEXT_TB<http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB>)

there is one MainTable/key pair listed at the top of the XML:

<MainTable>EXPRESSION_TEXT_TB_**_EXPRESSION_TEXT_TB__main</**MainTable>
<Key>OID_109_key</Key>

However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text"
field="oid_108" hideDisplay="true"**internalName="oid_108_filter"
key="OID_108_key" legal_qualifiers="like" qualifier="like"
tableConstraint="main"/>

And

<AttributeDescription default="true" displayName="Emage ID"
field="accession_1037" internalName="accession_1037"**key="OID_1037_key"
linkoutURL="http://www.**emouseatlas.org/emagewebapp/**
pages/emage_entry_page.jsf?id=**EMAGE:%s" maxLength="20"tableConstraint=*
*"main"/>

Since these filters and attributes refer to keys about which no
information is provided in the XML, they can not be recreated by 0.8 and are
ignored.

4. and 5. BioMart 0.8 does not currently have these capabilities, but they
are planned for future releases.

Sincerely,

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:         <a moz-do-not-send="true" href="tel:647-260-7818" value="+16472607818" target="_blank">647-260-7818
Toll-free: <a moz-do-not-send="true" href="tel:1-866-678-6427" value="+18666786427" target="_blank">1-866-678-6427
www.oicr.on.ca<http://www.**oicr.on.ca<http://www.oicr.on.ca>>



On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:

I was looking at http://central.biomart.org/ after reading the recent
paper in Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE
biomart included in there.
However I have some quibbles about how the EMAGE interface has been
represented on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters
and attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing
a v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8
release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--


--
Peter Stevenson         | [hidden email]
EMAP Computer Support   | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: <a moz-do-not-send="true" href="tel:%2B44%20%280%29131%20332%202471" value="+441313322471" target="_blank">+44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |




_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users