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 <[email protected]<mailto:[email protected]>> Date: Wed, 28 Sep 2011 06:13:10 -0400 To: Arek Kasprzyk <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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/**<http://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<tel:647-260-7818> Toll-free: 1-866-678-6427<tel:1-866-678-6427> www.oicr.on.ca<http://www.oicr.on.ca><http://www.**oicr.on.ca<http://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 | [email protected]<mailto:[email protected]> EMAP Computer Support | http://www.emouseatlas.org/emage MRC Human Genetics Unit | Phone: +44 (0)131 332 2471<tel:%2B44%20%280%29131%20332%202471> Edinburgh EH4 2XU. U.K. |
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