ntm/idn

Interactomic data web navigator

idn's Issues

get DBcheck.pl to send email

no sendmail/exim is currently configured on ariane, get it working and test that the cronjob works and emails us as expected

psicquic queries within biomolecule report

Le problème d'interrogation via PSICQUIC persiste. Quelle que soit la requête effectuée seules les résultats issus des bases de données InnateDB, MPIDB and ChEMBL sont interrogées (cf. le mail du 4/02/2014)

import matrisome info

We want to import data from
http://web.mit.edu/hyneslab/matrisome/

Simple solution would be to use the existing Personal_Keyword tag in ?Biomolecule.
More detals in email sent today to SRB and GL.

experiment report: missing most data

la page "Experiment Report" est incomplète (au moins pour GAG_1et GAG_2, peut-etre pour tout le monde)

Gene Ontology additional column for term namespace

affiche results sur iNavigator

changer le mode d'affichage des resultat (overflow : hidden et text-elipsis

Import matrixdb curated through mitab service

mitab served by psicquic

nous sommes aussi serveur psicquic, et ce qu'on sert n'est pas a jour (tout comme ce qu'on propose dans la page download).
AFAICS il faudra simplement copier le nouveau fichier mitab dans
/usr/local/psiquic/psicquic-read-only/psicquic-webservice/mitab.txt
(et peut-etre relancer un service psicquic?)

Complexes: migrate from MULT_* to EBI identifiers

Have to find (or ask Sandra to create) an EBI identfiier for each current matrixdb MULT object. SRB must confirm that the MULT-EBI mapping is correct.
This is ongoing.

Then we wish to replace the MULT identifiers by EBI ones everywhere in matrixdb, keeping the old MULT_* names only as a ?Text field somewhere in ?Biomolecule (so it can be searched for with tace->grep).

iN

vig

ajout subdir

j'ai rajouté un subdir chez MD et sur le serveur:
matrixdb_InConstruction/data_Backbone/biomoleculeData/scriptMade/Orthologs/

Point Mutation amino acid types wrong usage

Dump and edit Experiment.ace to obtain one Feature per amino acid mutation, using the tag Name to mention the types
see example below.
Experiment => O08859__P26022_21619930_MatrixDB_1
3 Biological_Feature Point_Mutation Point_Mutation_Data
Name cys103ser
Range 1
Position_start
103
Status_start
certain_sequence_po
sition
Position_end
103
Status_end
certain_sequence_po
sition
Point_Mutation_Type
mutation_decreasing
_interaction
4 Biological_Feature Point_Mutation Point_Mutation_Data
Name
cys47ser_cys49ser
Range 1
Position_start
47, 49
Status_start
certain_sequence_po
sition
Position_end
47, 49
Status_end
certain_sequence_po
sition
Point_Mutation_Type
mutation_decreasing
_interaction

bug human only index

bug selection deselection sur more or less

import PPIs from intact et al, using psicquic in a cronjob

on veut importer, de maniere minimaliste, les PPIs qui concernent au moins une prot ECM/Secreted/Membrane, en provenance de Intact et sans doute d'autres sources psicquic.
Il faut donc:

1. un parser mitab -> matrixdb, qui utilise des tags appropriés pour la source;
2. un script qui

• fasse des queries psicquic,
• fasse une selection Quality Control (dans MIQL si possible, en post-traitement sinon) pour se limiter aux prots d'interet et se limiter aux PPIs "solides" et binaires et ignorer les PPIs qu'on a deja dans matrixdb (?),
• parse le mitab obtenu avec 1,
• sauve le .ace resultant quelque part (timestamped ace file).
• un cronjob pour lancer ce script 2 regulierement, et soit le parse dans matrixdb_latest, soit nous avertisse pour qu'on puisse checker le fichier avant de le parser (au moins dans un premier temps).

biomolecule report missing interactions

La page "Biomolecule Report" est incomplète pour les interrogations avec des identifiants UniProtKB, MULT-x et PFRAG-x. La liste des interactions ne figure plus sur ces pages (cf. les fichiers ci-joints).

Add imex status to bullet in publication hits

retet

zrezerzr

report footer

implement footer div to all report pages

comportement autofocus

autofocus does not count the hide nodes

Experiment Label Overlap in Experiment report

http://matrixdb.ibcp.fr:9999/cgi-bin/current/newPort?type=experiment&value=MULT_12_human__Q05793_11956183_MatrixDB_1

tooltip to species column

ree

teat

index accordeon

fix its behaviour,
bottom div round corners
click on collapsable div already shown should not trigger its collapse.

add "curation level" as title in relevant dataTables

MI CV hyperlink in partnerDetails html

AND retrieve the underscore from the litteral name

extend / refresh Controlled Vocabulary terms in models.wrm

SRB seems keen on altering the current CV terms stored in matrixdb in order to
synch them w/ current OLS content.

change association word by the less confusing one "interaction"

Kinetics_comment

bug on go term

GO:0010740 definition null et term null

Tooltip of publication in "affiche_result" no bound to body

Participant Name background color to refer to biomolecule type

hide result navigator

fix the comportement of afficheResult : no hide on click on page background

web page matrixdb-new: acknowledgments

ça me semble une bonne idée de rajouter une page acknowledgments où on peut remercier les differentes BDs dont on extrait de l'information. On pourrait aussi dans cette meme page indiquer quelle version / release / date de chaque BD source est utilisée dans matrixdb.

update psimi tab and xml files

Il faudra re-générer les fichiers psimi tab et xml, puis les deposer (avec un timestamp dans le filename) dans:
/var/www/matrixdb_1_live/html/download
et modifier les symlink latest de ce subdir pour qu'ils pointent dessus, et editer
/var/www/matrixdb_1_live/cgi-bin/download (date de release)

Homology relationship between association

fix href to inferred association.
Check cross ref.

missing PEPS ref in footer of report

responsive report stamps and partner table layout

Could be optimised to avoid blank between stamps region.
partner table could scroll down

add plural to barSearch hits category

autofocus on hidden node

autofocus prend en compte les noeud caché

iNavigatorGateway should use POST

models.wrm ambigious Inferred node tag

?Association Kind Genuine PMID ?Publication XREF Association
Experiment ?Experiment XREF Association
Inferred InferredFrom ?Association XREF Supports
Supports ?Association XREF InferredFrom

SHOULD BE RENAMED

?Association Kind Genuine PMID ?Publication XREF Association
Experiment ?Experiment XREF Association
Inferrance InferredFrom ?Association XREF Supports
Supports ?Association XREF InferredFrom

Range Data, start/stop position with mutliple positions

GAG_1__MULT_15_human_19502598_MatrixDB_5

                          MULT_15_human   BioRole     unspecified_role
                                          ExpRole     prey
                                          Detect_Meth     predetermined_participant
                                          Author_assigned_name    truncated alpha5beta1 integrin ectodomain
                                          Feature     1   Biological_Feature      Binding_Site    Binding_Site_Data
                                                                                                  Range   1
                                                                                                  Position_start
                                                                                                  1, 1
                                                                                                  Status_start
                                                                                                  certain_sequence_po
                                                                                                    sition
                                                                                                  Position_end
                                                                                                  613, 455
                                                                                                  Status_end
                                                                                                  certain_sequence_po
                                                                                                    sition
                                                                                                  Binding_Site_Type
                                                                                                  sufficient_binding_
                                                                                                    site

javascript code robustness to configurations unable to run glmol

eg: ubuntu + ff cant run the glmol renderer properly w/in the newPort context.
Perform a config chech or can the JS engine crash while page remaining functional?

test

contrenu

filter widget synchronization

When performing a second network search, the filter widget shall display
a "waiting for data" or "updating data" message.
Currently, it keeps on displaying the statistics of the previous network until suddenly
updating them once fetching is complete.
It should not be possible to use the widget filter until nodes,links fetching is complete.

bug on size network filter

when composant open during callback complete loading of data the table dont have the right size

navigue header

just keep the nav header on the same line

add head link to association to partner datable popup

interactome construction KO

checking one of the boses in criteria 1 - By localization , results in
The interactome can't be constructed (no available interactions for the query) !
Same result when using criteria 2 or 3, didn't test others...

Amino acid selection persist through PDB structure cycling

elementInfo widget and molecularViewer are to be fixed