Re: [ISAforum] How does nobody get started?

[Philippe]

Dear Bryan,

Thank you for reaching out and sorry for the delay getting back to you.

So you are making valid points.

There is no denying that our documentation may benefit from an update.

Unfortunately, as an academic project we don't have an enormous amount of time to spend on a highly polished documentation and it is not always straightforward to second guess users needs.

We'll take your observations on board.

With this out of the way, I will point you to 2 main resources:

1. our manuscript presenting the python API supporting the creation, validation and serialization of ISA objects to ISA-Tab, ISA-JSON and ISA-JSONLD.

https://doi.org/10.1093%2Fgigascience%2Fgiab060

We also have a jupyterbook available to give you a feel for using the API: https://isa-tools.org/isa-api/content/index.html

*warning*: we are aware this documentation does not reflect the latest release which has seen major rewriting and refactoring so be warn. We are currently working at updating it.

2. the release notes for the latest version of the API:

https://github.com/ISA-tools/isa-api/releases/tag/v0.14.2

This may provide you with a better overview what our efforts are currently focusing on.

A number of components are no longer maintained (ISAcreator, ISAconfigurator) or have been retired (BII web application). These are java applications, developed quite some time ago and are no longer supported.

We apologize for any inconvenience this may have caused you.

Should you decide to use any of our software output and wish to submit any questions, we'd be happy to assist as much as our availability allows.

We will however ask you on thing:

Please do make sure to read through this example of code of conduct  and, of course, abide by it before engaging again with us and if you'd like to receive further support.

Kind regards

Philippe

On 06/03/2023 16:05, Bryan Maloney wrote:

I've been directed to ISATools as a way to help my lab become compliant with the new NIH data management plan policy, which requires metadata. I sort of kind of get the inkling from surfing through the ISATools web site that this is one of the functions that it's supposed to do, but I can’t tell. I tried looking at the documentation—it seems to be incomplete and fragmentary. What is “ISA-converter”? What does it convert to? The supposed “docs” link goes somewhere that doesn’t mention ISA-converter, for example. Will I need ISA-converter for anything?

 

Likewise, there is no apparent actual manual for all this stuff. What’s the protocol for using ISA-whatever? Do I start with ISA-creator? Maybe? No? Can’t really tell. Do I have to instead start with ISA-creator configurator? How? I click the “docs” link and get sent to GitHub. However, when I click the “docs” link for ISA-creator, I get “This is a 404 error page”. Hooray? But when I click the “docs” link for ISA-converter, not a single mention of ISA-converter, but a page about BII web application????? Although, when I scroll down, there might appear to be (afraid to look) instructions for ISA-configurator and ISA-creator? When I click either of those, “perfunctory notes” might describe what’s there, but it doesn’t look like a manual.

Is ISATools just not ready to actually be used by anyone not within the Initiated Illumanati? I was hoping for something with a learning curve that was shallower and front-end loading that was lighter than "make it up myself". 

Is that available?

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Please, note that I share my time between 
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Dr. Philippe Rocca-Serra, PhD

University of Oxford, UK:
Associate Member of Faculty, Dep of Engineering Science;
R&D Group Co-Investigator: https://datareadiness.eng.ox.ac.uk
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Our latest papers: 
Machine Actionable Metadata Models and The FAIR Cookbook.
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ORCiD: 0000-0001-9853-5668
twitter:@Phil_at_OeRC

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