Hi just a pointer to a tool that makes a MAGETAB or tab2mage template for you which might be of interest. It's used by our submitters but you can download the template and use it locally. There's still a lot of manual filling in the sheet, but it seems to be used successfully by a lot of people and has recently been tested by NCICB caArray project who found it quite usable:
tab2mage http://www.ebi.ac.uk/cgi-bin/microarray/tab2mage.cgi MAGETAB http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi Validation is separate and the validator for either format can be found at http://sourceforge.net/project/showfiles.php?group_id=120325 Finally I read about KuteBase who have reworked the data upload workflow to BASE and built a batchuploader: http://vortex.cs.wayne.edu/taxonomy/term/69 cheers Helen Philippe wrote: > Hi Micha, Everyone > > I can somewhat relate to your experience that data entry from users > point of view. It is an issue as most biologists feel it is too time > consuming. > I think the idea of having a wizard helping create a tab2mage file would > help. Whithin NuGO consortium, the idea also came up during a recent > meeting. > My experience is that it should not take too long to create the wizzard > able to create a tab2mage file and then reuse the current code. > Also, Dominic has now included a validation mode which reports on all > pbs on the incoming tab2mage document which makes fixing easier and > increases the rate of successful loadings > Now with base2.5 in sight, we have to bring it in line with the recent > changes to data file management. > > My experience in NuGO for creating tab2mage file is a mix bag. With > proper guidance, people are pretty much able to create decent file quite > quickly. use in combination with the validation mode > life is a lot easier. But there are also people who just can't be bothered. > > Now comparing BASE2 and MIAMExpress may not be so straitghtforward. > There is a entire curation team backing up submissions and data entry > (both for Miamexpress and tab2mage submissions) and with a publication > at stake, people are ready to go through some level of pain to get > there. :) > This is really a bit of catch-22 situation. Everybody want properly > annotated datasets with loads of metadata but when it comes to biting > the bullet and entering information, well.... > > But you made a good point that having a wizard to create a tab2mage file > would help. I have been working on perl script (too ugly to show) that > just does that after having asked a few questions to the users. This is > probably something we can explore as it would certainly remove a number > of repetitive actions which are currently putting people off. > > Finally, this seems to be pointing to another need: Why not considering > a BASE training course ? > this sounds expensive but BASE2 is a complex system that delivers good > service provided one just does not walk away after spending 5 minutes on > it. > A lot of time has been spent in the documentation and there is a HUGE > amount of information in there but people hardly read it. and that's > probably a missed opportunity. > > cheers > > Philippe > > > > > Micha Bayer wrote: > > >> Hi, >> >> I gave a BASE2 talk and demo the other week at a sister institute of >> ours where they are considering introducing BASE2, and the feedback we >> got from users there -- and from users at our own institute -- was quite >> an insight into how things look from the user's perspective. >> >> Basically, the upshot of it is that getting data into BASE is still so >> difficult that it puts people off using BASE, and that is even with the >> Tab2Mage importer (they did like BASE otherwise though!). At the demo >> one of the users said that he had been trying to make a Tab2Mage >> spreadsheet (by hand) to submit to ArrayExpress, and basically gave up >> on it because it was way too difficult (this case did not involve BASE). >> >> >> At our own institute here we have decided not to let lab biologists near >> BASE at all because it is well beyond their level of computer literacy, >> and instead all our data handling is done by a single admin-type guy >> (himself a biologist but fairly computer literate). >> >> However, even he came very close to giving up on BASE completely after >> trying to manually put data for his first MIAME compliant experiment >> into BASE (that's with me helping him), and he kept on referring to the >> fact that he had previously submitted data to ArrayExpress using the >> MIAMEExpress web interface without having had any previous training or >> without reading a manual. >> >> We didn't use the Tab2Mage importer on that occasion because a) it still >> has major issues that need fixing before it's ready for production use, >> b) because our admin guy felt that Tab2Mage was too complicated for his >> liking, and c) because we felt that it would probably aid our >> understanding of BASE to do it manually, at least the first time round. >> >> So there are a number of conclusions to be drawn from this and from my >> previous experience of writing stuff for biologists: >> >> 1. Levels of computer literacy in the biologist community are low, >> especially compared with physicists and chemists etc. >> 2. If stuff is too difficult to use, biologists do not use it and >> instead go back to their old ways (copy-and-paste, data in files without >> any backups, that sort of thing). >> 3. Users don't read the manual. >> 4. A significant effort is required to make the data entry into BASE >> easier than it is at the moment, and that includes the Tab2Mage import. >> >> Personally, I come from a school of thought that works along the lines >> of "the customer is always right". I believe firmly that if we cannot >> make people use our software then we may as well not bother writing it >> in the first place. >> >> My immediate ideas for making some progress here are: >> >> - Write a BASE plugin that basically uses a lot of the Tab2Mage importer >> code but bypasses Tab2Mage completely, and instead gathers the required >> info for the entire experiment through the BASE user interface (i.e. the >> plugin dialog) in a well-annotated fashion that requires no previous >> training or reading of manuals, and then imports the raw data files from >> a zip file. >> >> OR >> >> - Write a separate, standalone web application that basically talks the >> user through the process of making a Tab2Mage spreadsheet and writes the >> user input to a tab2mage file in the background. The user can then >> download this and import their data into BASE using the Tab2Mage >> importer. This scenario obviously depends on the outstanding issues with >> the Tab2Mage importer to be fixed, and for it to be maintained too. >> >> I think the web application scenario is perhaps the better one in terms >> of component reuse, as it doesn't require any more code to be written >> than is really necessary, and we would be happy to write and host this >> at our end here (and of course pass it on to anyone who wants to host it >> locally at their end). I also think it would be useful for non-BASE >> users that want to just manually make a Tab2Mage spreadsheet and submit >> it to ArrayExpress. >> >> Sorry -- this has been a bit of an epic rant, but I think there is an >> urgent need for discussion (and then action!) here. >> >> Cheers >> >> Micha >> >> >> ================================== >> Dr Micha M Bayer >> Bioinformatics Specialist >> Genetics Programme >> The Scottish Crop Research Institute >> Invergowrie >> Dundee >> DD2 5DA >> Scotland, UK >> Telephone +44(0)1382 562731 ext. 2309 >> Fax +44(0)1382 562426 >> http://www.scri.ac.uk/staff/michabayer >> ================================== >> >> >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> >> SCRI, Invergowrie, Dundee, DD2 5DA. >> The Scottish Crop Research Institute is a charitable company limited by >> guarantee. >> Registered in Scotland No: SC 29367. >> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. >> >> >> DISCLAIMER: >> >> This email is from the Scottish Crop Research Institute, but the views >> expressed by the sender are not necessarily the views of SCRI and its >> subsidiaries. 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