msi-workgroups-data-processing — This is the list for the msi data processing WG

[Msi-workgroups-data-processing] MIBBI published in August's Nature Biotechnology

[Susanna-Assunta S. <sa...@eb...>]

Dear colleagues,

We would like to inform you that the paper describing the Minimum
Information for Biological and Biomedical Investigations (MIBBI) project
-- http://www.mibbi.org/ -- has been published this month in Nature
Biotechnology. This represents a significant step towards a comprehensive
set complementary reporting guidelines for the biosciences; both by
describing our work to date, and by acting as a beacon for new
participants.

A PDF of the paper is freely-available for download:
http://www.nature.com/nbt/journal/v26/n8/pdf/nbt.1411.pdf

This paper:
1. Describes the foundational work performed by the ever-growing list of
participants in this project.
2. Provides analysis of the various MI specifications registered at the
site (scope, conflicts, etc.), including the MSI's CIMR
3. Addresses the view of funders and publishers on the enforcement of
consensual reporting guidelines.
4. Outlines our plans for future work, which all are strongly encouraged
to monitor, and in which all are invited to participate.

 Any questions can be directed to:
 Chris Taylor
 Susanna-Assunta Sansone
 Dawn Field

 Yours Sincerely,

 Susanna, Chris and Dawn, on behalf of all authors.

 --

[Msi-workgroups-data-processing] Data transformation terms - discussion

[Susanna <sa...@eb...>]

Dear Stys,

I am fw your reply to me to the lists - in particular the Ontology and 
Data Processing WGs- so they are e able to comment on this.

Thanks,
Susanna

Dalibor Stys wrote:

> Dear All,
>
> I believe that simple definitions of data transformation are 
> dangerous. These methods are developing, we, for example, in our 
> Expertomica software for chromatography-mass spectrometry use adaptive 
> noise filtration and subtraction of backgroun in each data point. That 
> means that we analyse the information content of the data and subtract 
> the random noise, spikes and the background contributions separately. 
> This is principially impossible to describe by simple terms but it is 
> quite similar to what a qualified operator is doing, i.e. considering 
> how good are the data surrounding each peak and assessing the baseline 
> and the precision by which data may be integrated. We have 
> algoritmised the operator knowledge, added mathematical description of 
> noise and do it automatically.
> Other programs, i.e. Hyperchem, ask you to introduce couple of 
> parameter defined precisely only as mathematical equations inside the 
> program, which are then used for data transformation.
> This is true for MS, NMR, but in principle for any dataset.
> I, actually, suggested some terms but the more I think about it, the 
> more I do not like it. The only absolutely correct way would be the 
> reference to place where the original data may be downloaded, the 
> reference to the software and to all parameters which were used in 
> data analysis.
>
> Best regards
>
> Dalibor Stys
>
> Susanna-A Sansone wrote:
>
>> Dear Ontology and Data WGs,
>>
>> We are collecting these terms for MSI and then feed these in 
>> FuGO/OBI,  here is more info for you:
>>
>> *Definition for Data Transformation* (up for discussion):  The 
>> process of redefining data based on some predefined rules. The values 
>> are redefined based on a specific formula or technique.  This 
>> includes mapping data elements from from a source data format into 
>> destination data.
>>
>> *An example:*
>> NAME:  low_intensity_filter DEF:  A transformation method that 
>> involves removal of low intensity values in a data set.  For 
>> microarrays and gels the threshold for exclusion is usually based on 
>> some estimation of local or global background intensity; for mass 
>> spectrometry and NMR, it is usually based on the signal-to-noise 
>> ratio in the spectrum.
>>
>> Can you please send Daniel your tems, as a tab-delimited file with 
>> the following information in the file:
>>
>> Person Submitting:
>> NAME: DEF:
>> NAME: DEF:
>> NAME: DEF:
>> etc.
>>
>> Thanks,
>> Susanna
>>
>>
>> Susanna-A Sansone wrote:
>>
>>> ***sorry for cross-posting***
>>>
>>> Dear Ontology and Data WGs,
>>> (cc to Exchange, Chemical, Biology WGs fyi)
>>>
>>> We are in the process of collecting terms for **data 
>>> transformation** terms.
>>>
>>> Please, send your list of terms and definitions (if you have these) 
>>> to Daniel Schober -here cc- in an excel sheet.
>>>
>>> Thanks,
>>> Susanna
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>>
>>   
>

-- 
Susanna-Assunta Sansone, PhD

NET Project - Coordinator

www.ebi.ac.uk/net-project
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  room: A229            

  

[Msi-workgroups-data-processing] Data transformation terms - example

[Susanna-A S. <sa...@eb...>]

Dear Ontology and Data WGs,

We are collecting these terms for MSI and then feed these in FuGO/OBI,  
here is more info for you:

Definition for Data Transformation (up for discussion):  The process of 
redefining data based on some predefined rules. The values are redefined 
based on a specific formula or technique.  This includes mapping data 
elements from from a source data format into destination data.

An example:
NAME:  low_intensity_filter DEF:  A transformation method that involves 
removal of low intensity values in a data set.  For microarrays and gels 
the threshold for exclusion is usually based on some estimation of local 
or global background intensity; for mass spectrometry and NMR, it is 
usually based on the signal-to-noise ratio in the spectrum.

Can you please send Daniel your tems, as a tab-delimited file with the 
following information in the file:

Person Submitting:
NAME: DEF:
NAME: DEF:
NAME: DEF:
etc.

Thanks,
Susanna


Susanna-A Sansone wrote:

> ***sorry for cross-posting***
>
> Dear Ontology and Data WGs,
> (cc to Exchange, Chemical, Biology WGs fyi)
>
> We are in the process of collecting terms for *data transformation* terms.
>
> Please, send your list of terms and definitions (if you have these) to 
> Daniel Schober -here cc- in an excel sheet.
>
> Thanks,
> Susanna
>
>------------------------------------------------------------------------
>
>-------------------------------------------------------------------------
>Take Surveys. Earn Cash. Influence the Future of IT
>Join SourceForge.net's Techsay panel and you'll get the chance to share your
>opinions on IT & business topics through brief surveys - and earn cash
>http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
>
>------------------------------------------------------------------------
>
>_______________________________________________
>msi-ontology-devel mailing list
>msi...@li...
>https://lists.sourceforge.net/lists/listinfo/msi-ontology-devel
>  
>

[Msi-workgroups-data-processing] Data transformation terms - needed

[Susanna-A S. <sa...@eb...>]

***sorry for cross-posting***

Dear Ontology and Data WGs,
(cc to Exchange, Chemical, Biology WGs fyi)

We are in the process of collecting terms for *data transformation* terms.

Please, send your list of terms and definitions (if you have these) to 
Daniel Schober -here cc- in an excel sheet.

Thanks,
Susanna

[Msi-workgroups-data-processing] special issue of OMICS journal on data standards - announcement

[Susanna <sa...@eb...>]

**** Sorry for the multiple postings *****

Dear All,

This is just a note to flag the *special issue of OMICS journal on data standards*. 

The online version is *free* and available at the following URL:
 http://www.liebertonline.com/toc/omi/10/2;jsessionid=nWAx67n0VoVdcUfY8Z

It containts 20 invited articles, including a piece on MSI, MGED and PSI.

 Best regards,
 Susanna

 --
 Susanna-Assunta Sansone, PhD

 Project Coordinator

 The European Bioinformatics Institute (EBI)
 EMBL Outstation - Hinxton
 Wellcome Trust Genome Campus
 Cambridge CB10 1SD, UK