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This repo is the Planteome fork of geneontology.org AmiGO2 project. Issues in this repo should be reported only on AmiGO issues. Issues can be pushed upstream if relevant for GO.

License: BSD 3-Clause "New" or "Revised" License

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Asigned by Austin Meier

http://dev.planteome.org/amigo/search/annotation

If you see on the left side facet 'assigned by'.. there are two different assigned by styles for 'Austin'. Please make them consistent.

AmiGO 2: Gene Product Xref to external source

http://dev.planteome.org/amigo/gene_product/Ensembl_Plants:OS06G0275000

I think the synonym Ensembl_Plants, OS06G0275000should appear in Database section and hyperlink to external source... Gramene

Links to GitHub Issue trackers are not working

From @cooperl09 on October 15, 2015 17:51

Links to GitHub Issue trackers (ie PO_GIT; TO_GIT; EO_GIT; PSO_GIT) are not working. They show up in the "mappings" tab.

Copied from original issue: Planteome/planteome-core#15

Issue with curator definition DBX-Ref for Gramene curators

Notice a weird issue- where we have Gramene curators names in the definition DBX-Ref, Amigo is trying to create a link, but it goes nowhere. This is because we have the GR: Xref in our annotations.
Suggest we change the curator dbxref to Gramene: from GR: to avoid this issue.

examples:
GR:Pankaj_Jaiswal
GR:Anuradha_Pujar
GR:Chih-Wei_Tung

replace gene ontology specific instance in search result template

http://dev.planteome.org/amigo/medial_search?q=PO%3A0025470

IN THE SEARCH RESULTS 'ONTOLOGY' it says 'Gene Ontology....' in your template change it to 'Ontology.....' remove 'Gene'

Planteome: ontologies being loaded

http://dev.planteome.org/amigo/search/ontology

May need Chris and Seth's help here.

I just looked on the types of ontologies being loaded...

suggest dropping

quality (PATO) not sure if we need it here. If it is coming from cross products or helping Termgenie, I suggest for this release clean them out.
ECO
If we can import cassava ontology into TO as we showed a proof of concept in our workshop, then we do not need it to be loaded separately.

-can we merge go/extensions/gorel into external....the are both relations ontologies

avoid duplicating pato.ontology vs quality.........

Amigo browse tree

http://dev.planteome.org/amigo/dd_browse

May I suggest limiting the tree to IS-A only or have a selection of relationship_types to choose either configured by the admin or options available to users to select.

In a simple way I suggest starting only with IS-A and build on top of that.
@cmungall @elserj @kltm @cooperl09

Planteome: Ontology GO Alt ID links

http://dev.planteome.org/amigo/search/ontology

GO IDs in the Alt ID column on right link to GO website which does not return anything.

I suggest disabling this hyperlink. There is no need for that link since these IDs are coming from old terms that were merged to the new primary term.

We might have PO terms with Alt ID but did not check it.

AmiGO 2: Gene Product Details for Ensembl_Plants:AT4G38130

http://dev.planteome.org/amigo/gene_product/Ensembl_Plants:AT4G38130

please drop the go-ortholog file for A. thaliana from loading.

Synonym dbxrefs are not being displayed

In the plant structure development stage (PO:0009012) branch of the PO we have a large number of mappings from our stage terms to terms in other ontologies and vocabularies.
The corresponding mappings (eg GRO:ID) do not show up in the browser and you cannot search for them.

For example:
[Term]
id: PO:0007022
name: seed imbibition stage
namespace: plant_structure_development_stage
def: "A seed germination stage (PO:0007057) during which there is absorption of water by the seed (PO:0009010)." [Gramene:Anuradha_Pujar, ISBN:0306416875, POC:Laurel_cooper]
synonym: "0.1 imbibition in maize (related)" RELATED [MaizeGDB:64054]
synonym: "01 Beginning of seed imbibition in soybean (related)" RELATED [SOY:0000090]
synonym: "03 Seed imbibition complete in soybean (related)" RELATED [SOY:0000091]
synonym: "1.02-start of imbibition in barley (related)" RELATED [GRO:0007053]
synonym: "1.02-start of imbibition in oat (related)" RELATED [GRO:0007053]
synonym: "1.02-start of imbibition in Triticeae (related)" RELATED [GRO:0007053]
synonym: "1.02-start of imbibition in wheat (related)" RELATED [GRO:0007053]
synonym: "1.03-imbibition complete in barley (related)" RELATED [GRO:0007054]
synonym: "1.03-imbibition complete in oat (related)" RELATED [GRO:0007054]
synonym: "1.03-imbibition complete in Tricticeae (related)" RELATED [GRO:0007054]
synonym: "1.03-imbibition complete in wheat (related)" RELATED [GRO:0007054]
synonym: "BBCH growth stage 01 (related)" RELATED [ISBN:3826331524]
synonym: "imbibition in Arabidopsis (related)" RELATED [TAIR:0000394]
synonym: "imbibition in Solanaceae (related)" RELATED [SGN:0000004]
xref: PO_GIT:366
xref: PO_GIT:595
is_a: PO:0007057 ! seed germination stage

Is there a way to display these in the Planteome browser?

putting search box on the homepage

is there a way to put the search box we see on the right hand side on http://browser.planteome.org/amigo/search/annotation on the www.Planteome.org homepage

GR_gene Xref need fixing

http://dev.planteome.org/amigo/gene_product/GR_gene:60333

looked at http://palea.cgrb.oregonstate.edu/viewsvn/associations/to-associations/to_Gene_association.assoc?revision=679&view=markup

actual object_ID is 'GR:0060141'
If it is used as above the link to Gramene would work
like

http://archive.gramene.org/db/genes/search_gene?acc=ID
e.g
http://archive.gramene.org/db/genes/search_gene?acc=GR:0060333

replacing ID with GR:0060333
The existing URL e.g. from this page http://dev.planteome.org/amigo/gene_product/GR_gene:60333 is missing the prefix 'GR:00' from the ID

Base_Statistics - add new aspects to "annotations by aspect/species by evidence"

Trying to add non-GO aspects to "base_statistics" graph for annotations by aspect, and it doesn't seem to be as easy as I hoped.

I've modified the javascript/web/BaseStatistics.js file where I think it needs to be, and they show up on the axis, but no annotations are actually picked up. I assume I need to make some other change to get it to recognize the new aspects, but not sure where it would be.

AmiGO 2: Term Details for some links

http://dev.planteome.org/amigo/term/EO:0007359

Related
to all genes and gene products annotated to plant experimental condition.

replace 'genes and gene products' with 'annotated objects' in your templates.

Existing one is GO specific.

Pankaj

Japanese not displayed properly in term page

The Japanese synonyms show up properly on the main page (http://dev.planteome.org/amigo/search/ontology), but not on the term page (http://dev.planteome.org/amigo/term/PO:0025034). They do show up properly if the user changes the encoding setting on their browser.

Relations are not being recognized and displayed in AmiGO 2.0

From @cooperl09 on January 17, 2016 1:59

Currently, there are a limited number of relations being recognized by AmiGO 2.0:
is_a
part_of
occurs_in
In the Plant Ontology file, we have a number of important relations that are missing in the browser view:

Relations with examples:

[Typedef]
id: adjacent_to
name: adjacent_to
xref: RO:0002220

e.g. id: PO:0025382!
name: substomatal cavity
relationship: adjacent_to PO:0008032 ! stomatal pore

[Typedef]
id: derives_by_manipulation_from
name: derives_by_manipulation_from

e.g.
id: PO:0000007 leaf-derived cultured plant cell
relationship: derives_by_manipulation_from PO:0025034 ! leaf

[Typedef]
id: develops_from
name: develops_from
xref: RO:0002202
is_transitive: true

e.g.
id: PO:0000015
name: cotyledon primordium
relationship: develops_from PO:0025432 ! cotyledon anlagen

[Typedef]
id: has_part
name: has_part
xref: BFO:0000051
is_transitive: true

e.g.
id: PO:0009049
name: inflorescence
relationship: has_part PO:0009046 ! flower

[Typedef]
id: has_participant
name: has_participant
xref: BFO:0000057

e.g.
id: PO:0007033
name: whole plant development stage
relationship: has_participant PO:0000003 ! whole plant

[Typedef]
id: located_in
name: located_in
xref: RO:0001025

e.g.
id: PO:0025281
name: pollen;
relationship: located_in PO:0025277 ! pollen sac

[Typedef]
id: participates_in
name: participates_in
xref: BFO:0000056

e.g.
id: PO:0000423
name: plant zygote
relationship: participates_in PO:0001097 ! plant zygote stage

[Typedef]
id: preceded_by
name: preceded_by
xref: BFO:0000062
is_transitive: true

e.g.
id: PO:0001040
name: dry seed stage
relationship: preceded_by PO:0007632 ! seed maturation stage

[Typedef]
id: precedes
name: precedes
xref: BFO:0000063

e.g.
id: PO:0001078
name: plant embryo cotyledonary stage
relationship: preceded_by PO:0004507 ! plant embryo bilateral stage
relationship: precedes PO:0001081 ! mature plant embryo stage

Copied from original issue: Planteome/planteome-core#20

allow/convert spaces inside relationships in column 16?

@cmungall is there a way to allow spaces in column 16?

We have lots of germplasm annotations that receive the relationship: "has_phenotype_score()" And the string that get's pulled from the Samara scrape file often has spaces in it. For example:

"Culm_diameter_(mm)_of_basal_internode_at_repro.=6"

Currently I am simply substituting spaces, and other illegal characters for "_". It works, but it looks really bad when displayed on the browser. I was wondering if there was a way to allow spaces if the string containing them falls inside the "( )" of the relationship. Or if there is something I can replace the spaces with that would be converted to spaces when viewing them in the browser (Think "%20" in URLs). In the above example the column16 from the GAF would look like:

has_phenotype_score(Culm%20diameter%20(mm)%20of%20basal%20internode%20at%20repro.=6)

That way the browser would display this as:

has phenotype score Culm diameter (mm) of basal internode at repro.=6

Let me know if this is not clear.

incorrect PO links on dev

PO links redirect to the old plant ontology browser on the planteome dev website (term ID column).
Here an example: http://dev.planteome.org/amigo/search/ontology?q=fruit

Issues with filters on the Ontology Search page

From @cooperl09 on October 15, 2015 16:54

User filters are not retained if you click on an ontology term, and then go back to the main page from it.

See: geneontology#50

Copied from original issue: Planteome/planteome-core#13

Cannot search for EO or PDO terms by ID #

From @seymourmegan on August 31, 2015 17:44

We are unable to look up EO or PDO terms by ID # in the TO,EO, PSO Dev browser.
http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/go.cgi

For example:
When I search for PDO:0000176, the dev browser returns nothing.
Sometimes it will find the PDO or EO ID in a definition and return that, but otherwise does not work.
Since this was originally just for the TO, it seems to be set only to find TO ids.

Copied from original issue: Planteome/planteome-core#3

uptime monitoring?

Working on the GBCR paper we discovered that it would be nice to have something external that does "uptime monitoring" of our sites. Should probably have it keep track of both the drupal and AmiGO sites.

GO uses "Uptimerobot site monitoring".

Add summary line to bottom of term detail page to list out annotation functions

AmiGO 2: ISBN Xrefs

http://dev.planteome.org/amigo/term/PO:0005849

Suggest directing the ISBN Xrefs to
http://www.isbnsearch.org/isbn/XXXXX

XXXXX replaced by the ISBN ID digits

e.g.
http://www.isbnsearch.org/isbn/0122151704

Planteome: Search cassava germplasm annotations

http://dev.planteome.org/amigo/search/annotation?q=*:*&fq=assigned_by:%22marie-angelique_laporte%22&sfq=document_category:%22annotation%22

needs fixing the GAF annotation file.

fill object name column. if no data available, replicate the info from object symbol column
some direct annotation data shows up as TO ID vs others with TO term name. Not sure where the fault is. Whether it is so in the GAF file or it's a Amigo display issue

on this page
http://dev.planteome.org/amigo/gene_product/Genesys:CM840-177
the synonym should not have a hyperlink.

link the Genesys:CM840-177 hyperlinked to genesys database website.

Synonym scopes are not being displayed- AmiGO 2.0

From @cooperl09 on December 12, 2015 23:51

Synonym types are not being displayed in the AmiGO 2.0 browser. For example see fruit: http://dev.planteome.org/amigo/term/PO:0009001

The types of synonyms are listed here: http://wiki.plantontology.org/index.php/PO_Developers_Guide#Synonyms

For example:
narrow: accessory fruit
narrow: achene
narrow: acorn
narrow: aggregate fruit
narrow: akene
narrow: anthocarp
narrow: berry
broad: diaspore

Copied from original issue: Planteome/planteome-core#17

Annotated images in AmiGO

Wish list for image annotation work.

Blocked by upstream geneontology#368. More info at that issue tracker.