phenoscape / phenex Goto Github PK

Report for characters and character states that are missing annotations. Thus, when a curator skips a character, the program would report e.g., 'missing annotation for character(s) 44, 45 ,99'; or when a curator misses annotating a character state (e.g., annotates state 1 but not state 0), it would report 'missing annotation for character 45, state 0'.

Phenex contains reusable code, which should be made part of a broadly useful library, which would then also be used by the Phenex application.

@hlapp

Excluding size

cartilaginous and ossified are in PATO but not available in Quality field in Phenex

check that bearer_of relates Entity to Quality and that inheres_in relates Quality to Entity

In the exported file, some entities do not match their parent attribute term. For example, Quality: decreased length goes up to Pato: 'quality' rather than Pato'size'. There are other examples as well.

Wasila and Alex

Various per-matrix-cell values would be useful:

• evidence code
• coding interpretation (basic observation, ancestral state, class assertion)

I comfirmed and closed the request for the matrix tabbing but saw that there were comments in that request for this feature to apply to all panels:

Date: 2008-10-02 15:04
Sender: pmabee

The curators at the SD workshop really wanted the tabbing feature through
the Phenex interface (e.g. in the Phenotype panel to tab from Entity to
Quality etc.) as well as the above Data Matrix request.

this would be useful in all of the tables. Also, "tab to next cell" means
go to cell immediately to the right.

In the specimen section a comment box would be very useful as important information (such as if the specimen number conforms to a single individual or a lot, the ontogentic stage of an individual specimen) could be inserted there so future users can decide how they want to modify the original matrix to fit their goals.

Suggested by Melissa.

Using Phenex 1.5 with the data migration features, noticed that a post-composed entity appears as:
dorsal mesentary^null(swim bladder).( Fink and Fink 1981 character 57)

'null' should probably be 'part_of'

When a relational quality such as "fused with" is chosen for Quality,
enforce curation of a second entity ("related entity" in Phenex).

The cursor in the Dataset tab doesn't allow editing within already existing text. It jumps to the end of the text block. Need the dataset text box to be more editable.

Thanks,
@wdahdul

it would be helpful if the text was more obvious, with red font and larger (or bolder?) font. Perhaps just red color will suffice.

Also have the panel appear in the default layout so that we won't forget to use it.

Thanks!

In Phenex 1.4.1, Alex and I are finding that panels freeze or partially disappear (see screenshot) when scrolling or clicking among the panels. Also multiple rows are selected when we scroll through the character or states panels. These issues don't seem to be showstoppers so just reporting for now and we'll continue using this version.

Right now it is awkward to start a new file if the user has already opened one - essentially you need to quit and relaunch. There should be a "new" menu item.

After submitting a request (for "subcircular", subtype of PATO: circular, we noticed that the term info panel updated with this provision terms and its ID, but the provisional term wasn't available in the Quality field. We were assuming it should be available immediately in order to complete the annotation?

• Wasila

Need adjacent_to in the post-composition field. It's in teh relations ontology:
http://obo-relations.googlecode.com/svn/trunk/src/ontology/ro.obo

id: RO:0002220
name: adjacent to
def: "x adjacent to y if and only if x and y share a boundary" []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "belongs in BFO?" xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000004 ! independent continuant
is_a: RO:0002163 ! spatially disjoint from

When I open a new file at the same time that a cell in the old file is selected as editable, the new file will open with that same cell editable and term in the cell of the previous file gets carried over.

• @wdahdul

The links make it difficult to review EQs. Alex, Paula and I don't think they are necessary now.

With autosave enabled, you can't cancel out of Import > NEXUS popup window. Hitting cancel pops up the window again, while adding a character row.

Cancel works ok without autosave.

Thanks,
Wasila

Report the characters in which parent qualities are different between states of a character. This could be correct (due to multiple phenotypes per state) but in some cases could be a mistake by the curator.

Thanks,

Wasila

This happens when two people are working on the same file:

When accepting changes from another user, Phenex unselects the row that was selected prior to replacing the file, meaning that the user loses their position while working and it's very confusing. Ideally Phenex would accept the new changes while holding the current selection in place.

• @wdahdul

From Wasila:

Need a free text column called "Character discussion", which contains text that will be displayed in KB source box.

Thanks

Need to add "not" to list

Alex and I are experiencing Phenex freezing when using autocomplete in the phenotypes field or when manually saving the file. It takes several seconds for Phenex to become responsive.

We need a couple more features for editing matrices and taxon lists in Phenex, in cases where a NeXML file has been modified and a new import from Mesquite isn't feasible.

1. In matrix panel, be able to duplicate rows for additional taxa (e.g., in cases were a matrix taxon needs to be expanded out for all species examined).
2. In Taxa panel, be able to delete multiple rows of taxa, rather than only one at a time as currently restricted to.

Thanks,
Wasila and Dave

Specialized interfaces for particular types of EQs (presence/absence, relative, etc.).

Need an About panel showing version, etc.

Some characters are missing the states free text. See Brazeau 2009, characters 106, 107, and 108 for example.

When typing in an ontology field, the autocomplete drop-down menu has a fixed width in the Windows version (makes it difficult to see the complete term name), whereas the menu expands to show the term names completely on the Mac version.

Thanks,
Sandrine (and Wasila)

Add report that checks whether post-composed terms are nested correctly. It is very hard to check this manually. Most post-compositions should be nested. For example: "process(part_of(anterior region(part_of(maxilla))))" rather than "process(part_of(anterior region))((part_of(maxilla))". There are exceptions to this, but they are few, e.g., exception to this is a post-composition created to represent a joint: "joint^overlaps(metapterygoid)^overlaps(hyomandibula)". The curator can allow these exceptions.

This is on the Phenoscape wiki: http://phenoscape.org/wiki/Phenex#NeXML_file_format_extensions

First, each time I want to open Phenex, I have to open 2 files
("phenex-1.0.1-win" and "Phenex") and then I have to execute the MS-DOS
command file called "Phenex"... I don't have any Phenex icon which would
permit me to directly launch Phenex.

• Sandrine

For example, Nesbitt 2011 (Sereno file) cuts off at character 169.

Thanks

To ensure that identical characters in different publications are curated identically it would be ideal if we could open multiple files in different windows at the same time.

The Phenex web page needs to be reviewed and brought up-to-date ASAP.

Terms that have been automatically updated (provision term replaced_by permanent ID) retain a bright red font. See attached screenshot.

Would be great to right click with a mouse and copy/paste text from free text cells in Characters and States panels. Right now you can use the keyboard, but it would be quicker in some cases to use the mouse.

• Wasila and Sandrine