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ArrayExpress update--simplifying data submissions.

Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A - Nucleic Acids Res. (2014)

Bottom Line: The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold.ArrayExpress is a stable and highly accessed resource.Our future tasks include automation of data flows and further integration with other EMBL-EBI resources for the representation of multi-omics data.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.

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An Annotare sample submission form. In the Annotare submission system appropriate sample attributes can be chosen (e.g. disease, individual identifier, sex) and then populated either with terms selected from the Experimental Factor Ontology (EFO) or using free text. EFO terms are suggested as the user starts to type in a field. Samples can be easily added or deleted. Following sample creation submitters are guided through the assignment of labelling information for nucleic acid extracts in microarray submissions or library information such as the library layout in high-throughput sequencing submissions. Finally, users are guided through the submission of their data files.
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Figure 1: An Annotare sample submission form. In the Annotare submission system appropriate sample attributes can be chosen (e.g. disease, individual identifier, sex) and then populated either with terms selected from the Experimental Factor Ontology (EFO) or using free text. EFO terms are suggested as the user starts to type in a field. Samples can be easily added or deleted. Following sample creation submitters are guided through the assignment of labelling information for nucleic acid extracts in microarray submissions or library information such as the library layout in high-throughput sequencing submissions. Finally, users are guided through the submission of their data files.

Mentions: Annotare uploads the data files from the submitter's directory and captures experimental metadata through a series of spreadsheet-based web forms (see Figure 1), guiding the submitter step by step when constructing a submission. To allow efficient population of the forms, auto fill-down and copy-and-paste functionalities have been implemented, which are particularly useful for experiments with large numbers of samples. For instance, if many samples in the experiment are of the same species, the species field needs to be filled only for the first sample, whilst the others can be propagated down with a single click. Standard terms from EFO are offered in dropdown lists where possible, to encourage the use of standardized vocabulary at the point of submission. A validation step is built in to check all the information and files provided prior to executing the submission. The validation step would catch errors such as missing data files for an assay or the absence of attributes for samples, at which point the submitter can make amendments. After validation, Annotare generates MAGE-TAB files, which contain the experiment's metadata, and submits these together with the data files to ArrayExpress, where the accession number is provided to the submitter.


ArrayExpress update--simplifying data submissions.

Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A - Nucleic Acids Res. (2014)

An Annotare sample submission form. In the Annotare submission system appropriate sample attributes can be chosen (e.g. disease, individual identifier, sex) and then populated either with terms selected from the Experimental Factor Ontology (EFO) or using free text. EFO terms are suggested as the user starts to type in a field. Samples can be easily added or deleted. Following sample creation submitters are guided through the assignment of labelling information for nucleic acid extracts in microarray submissions or library information such as the library layout in high-throughput sequencing submissions. Finally, users are guided through the submission of their data files.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383899&req=5

Figure 1: An Annotare sample submission form. In the Annotare submission system appropriate sample attributes can be chosen (e.g. disease, individual identifier, sex) and then populated either with terms selected from the Experimental Factor Ontology (EFO) or using free text. EFO terms are suggested as the user starts to type in a field. Samples can be easily added or deleted. Following sample creation submitters are guided through the assignment of labelling information for nucleic acid extracts in microarray submissions or library information such as the library layout in high-throughput sequencing submissions. Finally, users are guided through the submission of their data files.
Mentions: Annotare uploads the data files from the submitter's directory and captures experimental metadata through a series of spreadsheet-based web forms (see Figure 1), guiding the submitter step by step when constructing a submission. To allow efficient population of the forms, auto fill-down and copy-and-paste functionalities have been implemented, which are particularly useful for experiments with large numbers of samples. For instance, if many samples in the experiment are of the same species, the species field needs to be filled only for the first sample, whilst the others can be propagated down with a single click. Standard terms from EFO are offered in dropdown lists where possible, to encourage the use of standardized vocabulary at the point of submission. A validation step is built in to check all the information and files provided prior to executing the submission. The validation step would catch errors such as missing data files for an assay or the absence of attributes for samples, at which point the submitter can make amendments. After validation, Annotare generates MAGE-TAB files, which contain the experiment's metadata, and submits these together with the data files to ArrayExpress, where the accession number is provided to the submitter.

Bottom Line: The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold.ArrayExpress is a stable and highly accessed resource.Our future tasks include automation of data flows and further integration with other EMBL-EBI resources for the representation of multi-omics data.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.

Show MeSH