nfdi4health / ldh

FAIRDOM-SEEK

License

Copyright © 2009-2023, University of Manchester and HITS gGmbH

BSD 3-clause

About FAIRDOM-SEEK

The FAIRDOM-SEEK platform is a web-based resource for sharing heterogeneous scientific research datasets,models or simulations, processes and research outcomes. It preserves associations between them, along with information about the people and organisations involved. Underpinning SEEK is the ISA infrastructure, a standard format for describing how individual experiments are aggregated into wider studies and investigations. Within SEEK, ISA has been extended and is configurable to allow the structure to be used outside of Biology.

FAIRDOM-SEEK is incorporating semantic technology allowing sophisticated queries over the data, yet without getting in the way of your users.

For an example of FAIRDOM-SEEK please visit our Demo.

To see FAIRDOM-SEEK being used for real science, as part of FAIRDOM please visit FAIRDOMHub

For more information please visit: SEEK for Science

FAIRDOM

FAIRDOM-SEEK is being developed and funded as part of the FAIRDOM initiative. For more information please visit: FAIRDOM.

Installation

We recommend installing FAIRDOM-SEEK on Debian or Ubuntu.

To install the latest release please visit: SEEK install guide

For details about other distributions and installing on Mac OS X please visit: Other distributions guide

The documentation is available on the ghpages branch.

Contacting Us

For details about how to contact us, to raise bugs or offer suggestion, please visit Contacting Us

Contributing to FAIRDOM-SEEK

In general :

1. Fork it ( https://github.com/seek4science/seek/fork )
2. Create your feature branch (git checkout -b my-new-feature)
3. Commit your changes (git commit -am 'Add some feature')
4. Push to the branch (git push origin my-new-feature)
5. Create a new Pull Request

For more details on how and what you can contribute to SEEK please visit Contributing

ldh's Issues

Investigation position unclear

The field “Investigation position” needs to have an information icon because its purpose is not clear.

Upload a datafile to a project directly

When uploading a data file, it is possible to assign a project.

But for me as a user it would be more intuitive, if I could upload a datafile to a project directly, i.e. somewhere on the project page. I did not find such an option (red box):

Add contribution guidelines

Please describe how external parties can/should provide contributions. Will contributions be accepted? Will they be merged with the official SEK? Add a CONTRIBUTING.md.

LDH is very slow

Our LDH installation is very slow, do you have any hints? Additionally, there are often timeout errors.

Email wasn't send for project manager, only for admin

Project managers weren't notified by mail and therefore didn't react, only Admins were notified (but did not feel addressed).

Additionally, mails are only sent weekly, dialy would be better.

Option to display resource lists as html unordered lists

List in Tabs, like all projects of a person, are shown as only comma separated list. This looks confusing for many projects. it would be nice to display it as an unordered list in HTMl style.This looks confusing for many projects.

Improve search capabilities

General search option would be very beneficial. If you search within projects - investigations cannot be found, keywords have to be present in each entry to be findable.

Optimize registration form

Bring back HDO functionality from LHA

Would like to have full Human Disease Ontology functionality from LHA merged in LDH

Rights to edit investigations

Why I am not able to edit the investigation when I am assigned a ”creator” role? Only Ana Grönke had the option to edit the investigation.

Add User Documentation

Add NFDI4Health Branding and Funding Page

Inclusion/exclusion criteria

Inclusion/exclusion criteria are very important for physicians and will be hard to define in these fields. Display as parameters would be very helpful.

MDS Modules

Purpose of these fields is unclear.

ORCID as athentification scheme

Please ann ORCID as a possible athentification scheme, so new users won't have to go through a complex registration process.

Invitation of new project managers

I would like to see an option to invite (new) project managers for a (clinical) study.

Hide display of empty extended metadata

Count and show number of hidden attributes

Creating of organisms

Later I saw that the users can create their own organisms and add them to the project. I suggest to add a hint on that in the project management window. For instance: “If you cannot find the organism, you can create it here.”

Highlighting of errors would be helpful

(In the long entry mask, it is hard to get to the errornous element)

merge origin/seek-1.13-seek_custom_metadata

Group information with subtitles

Would it be possible to group this information with subtitles?

Suppress "organisms" attribute view if "Organism" is disabled in settings

Can be seeen in Project lists "Organisms: Not specified"

RDF dcat enrichment

Guideline for LDH use

Graphical overview which type of data can be uploaded where – order of creation would be helpful

Improve adding tags

Specifying the project and assigning tags to the data worked without any complications. the tags were accepted (highlighted in grey) when I typed a comma.

In the following window, the tabs for “data type” and “data format” were only accepted (highlighted in grey) when I clicked somewhere else. It would be nice, if it worked with separating commas here too. Alternatively, I would suggest to indicate that an entry can be confirmed by clicking somewhere else.

Difference between SEEK and LDH

What are the functional differences between LDH and the original SEEK? Why should I choose this repo? Please provide documentation.

Build and Push Docker Image

Use of common terminologies

Why free text? Use of common terminologies essential in order to make the data searchable.

AI-based prediction/image recognition models

Currently, the asset „Model“ only covers model types used to model the behavior of biological networks/ systems. However, I can imagine that many use cases nfdi4health wants to support do not only use such models but also AI-based prediction/ image recognition models like the one developed in the CUP Use Case. Will it be possible to also upload such AI-based prediction/ image recognition models in the future? For this new options for model type, format andf environment should be introduced... maybe even a new asset type to avoid too long drop down lists.

Structed data elements for study intervention type

Why free text?

Better ordering of Related Items

Order of Related Items currently rather arbitrary - People first. I wish I could influence the order, e.g. for Project : Investigations/Assay/Data/Doc/Pub/Programmes/People
At least Investigation should be first and default here.
app/views/general/_items_related_to.html.erb / resp. app/helpers/related_items_helper.rb

More flexible use of metadata templates

We would like to use the LDH for clinical studies but also basic research projects. The extended metadata templates would not be applicable for these research projects. A more flexible use of metadata templates would be very helpful – can users provide their own metadata templates?

"Save draft" option for investigation

I would like to see an option to save a draft of the form when adding a new investigation or study.

Enable Custom Metadata for NFDI4Health MDS