Hi and thank you for this wonderful extension. I cannot find the option allowing the switch to Ctrl+double click behavior. I tried to use the 1.8.3 version of the extension on both Chrome (116) and Firefox (117). Attaching a screenshot showing the available options for the extension. Thank you.

Describe the feature

In addition to selecting genes by double clicking or dragging, add another option that requires the control key (Windows) or command key (Mac) to be pressed during the mouse event. Double-clicking is a general way of selecting text and this additional feature would prevent a query from happening unless the user specifically wants it to, as determined by pressing ctrl/command. It can be annoying having the panel open up to say No gene information available whenever a double click happens.

** provide a pop up when PMIDs are selected to organism-specific gene pages**

so for example the PomBase suggestion would be:
https://www.pombase.org/reference/PMID:30355493

GO aspect is restricted to a single aspect

• It would be much better to be able to see all 3 simultaneously

(also the GO feature does not seem to work for pombe gene identifiers- all pombe genes are in the GO database)

Hi,
I love this. Is it possible to add for fission yeast and we will advertise to our community
(PomBase is one of the core GO contributing databases)
https://www.pombase.org/

Val

Gene-Info Box not popping up

Steps to reproduce the behavior:

1. Go to https://gene-info.org/workspace/
2. Copy-paste my gene list
3. Double-click
4. Nothing comes up, no error sign

Add Pfam regions to the information panel in addition to domains. This should be a separate section on the panel that can be toggled on and off independently from domains via the settings.

Allow users to control the ordering of sections on the information panel. The ideal way to implement this would be to enable dragging and dropping of the fields in the extension popup to determine the order they will appear on the information panel.

Describe the resource

• name and url

ProteomicsDB, https://www.proteomicsdb.org/

• what does it do and what makes it unique from data we already incorporate?

They have MS1-based protein expression information from many cells and tissues.

• how can we download the resource programmatically and in what format(s)?

API endpoint (currently disabled). For tissues categories, change TISSUE_CATEGORY_SELECTION to 'cell+line' or 'tissue'. Change TAX_CODE for other species.

• what species does it support?

Humans: 9606
Arabidopsis: 3702

• how are database entries indexed (e.g. Uniprot accession, official gene name, etc)?

Entries from the endpoint are indexed by UniProt accession.

Additional context

• expression information is available numerically as NORMALIZED_INTENSITY and qualitatively (low, medium, high) as EXPRESSION_LEVEL
• parse ProteomicsDB identifiers from UniProt entry for linking (currently only available in UniProt for human entries - Arabidopsis will be added on their next publication)
• link format https://www.proteomicsdb.org/proteomicsdb/#protein/proteinDetails/79108/expression

It would be fantastic if when double clicking it was possible for the window to also contain information regarding your genotype pulled form a locally held raw data file. Much like what an old Firefox plugin did called SNPTips used to do. This would make it quicker and easier for people interested in genetics to check and compare their genotypes.

SNPTips on GitHub - https://github.com/belvario/snptips
SNPTips example video - https://www.youtube.com/watch?v=4d6Vs3PNE_g

It would be excellent to extend the use of the extension to most common bacterial species. Inclusion of E.coli and Salmonella would certainly broaden the potential userbase of the tool.

Safari 14 will support the Web Extensions API allowing for porting from Firefox or Chrome. See Safari Web Extensions.

Port the extension once 14 is out of beta (scheduled for fall).

Include instructions in documentation on how to modify the word separator for selecting text via double-click.

In Firefox: layout.word_select.stop_at_punctuation can be set to true

In OSX: changes with every OS release

Windows: ?

Linux: ?

Edge cases

• quotation marks
• terminal periods

Really nice work with this tool. Allowing users to sort the interactors list, either by BioGRID or IntAct evidence, could help to pick out top hits from the list.

Wormbase IDs

• e.g. WBGene00000536
• always prefixed with WBGene

Coding sequence (CDS)

• e.g. ZC395.2 and Y46C8AL.9a:wp261
• possible regex: \w+\.\w+(?::wp\d+)?
• this is referenced as ORF in UniProt
• can currently query by this by turning off autodetect and setting the query type to ORF
• is not currently autodetected

App is not launching upon selection

The following error is seen:

An error occured. Please use our issue tracker to report bugs.

Currently users can only hit the enter key to submit a search on the extension popup.

Should also have a button for submitting.

I routinely generate HTML report that have tables embedded with in them. I found that GIX works flawlessly when I use Firefox to open the HTML report, however, it fails when the report is opened in Chrome citing that 'Either your browser does not allow queries on this page, or you may need to hit refresh if you've just installed the extension.' Is it possible to extend HTML support to Chrome?

Thank you,
NM