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Nick Bargnesi
@nbargnesi
I think I see what you're saying. API defaults to http://localhost:9292/api now, defaulting the belmgr build BASE_URL to the same would give the out-of-the-box experience. Yes, that works. As long as no one tries to use a build artifact for anything other than that deployment.
Tony Bargnesi
@abargnesi
I think so. We can certainly package up the web application files in a single sub directory. Then we could serve them up through sinatra as static files.
At a different path.
Maybe belmgr could read the base url from the OpenBEL API configuration file. Use the configuration file as a central point of configuration data.
Puma could be setup with this configuration as well. That would get us towards needing only a rack-compliant http server once we can run on other rubies.
Nick Bargnesi
@nbargnesi
Then let's build artifacts for stable branches and releases on the build server. We'll publish the release artifacts to GitHub too. That supports the out-of-the-box experience and gem, Puma, etc, can use them directly. We do still need a reasonable default BASE_URL if none exists though. And the window.location scheme works well for this. If this sounds good, I'll write it up.
Tony Bargnesi
@abargnesi
Great idea! Sounds good to me.
I'll publish the build that I have now for 0.2.0. And I'll log a bug for "gulp build export" usage.
Nick Bargnesi
@nbargnesi
Can I link this discussion to the issue?
Tony Bargnesi
@abargnesi
No, don't think so. Gitter's API is mostly crap.
Paste it in?
Nick Bargnesi
@nbargnesi
Will do.
Woohoo! The timestamp to the right can serve as a link.
+1 gitter
Tony Bargnesi
@abargnesi
Super cool and impressive.
William Hayes
@wshayes
:point_up: March 16, 2016 9:58 AM https://www.linkedin.com/groups/4257384/members/admins Ted and Diane are the group admins. I’ll contact Ted and ask for you and I to be added.
Nick Bargnesi
@nbargnesi
Nice use of linking there :)
Tony Bargnesi
@abargnesi
Thanks william, thanks for the conversation reminder ;)
Nick Bargnesi
@nbargnesi
@abargnesi OpenBEL/belmgr#52
Tony Bargnesi
@abargnesi
@nbargnesi Attempted class inheritance comparison in OpenBEL/parsers@db85d81
PTAL
Tony Bargnesi
@abargnesi
@all I posted an early bel_parser (version 1.0.0.alpha.1) to RubyGems. https://rubygems.org/gems/bel_parser
Tony Bargnesi
@abargnesi
Install with gem install bel_parser --pre. You can then type BEL 2.0 terms into the console using the bel2_termcheck command.
Tony Bargnesi
@abargnesi
@wshayes Looked into PSI-MOD protein modification ontology (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo.xml). The root term is named "protein modification".
Seems to jive with how you named it.
William Hayes
@wshayes
Looking at the RDF Schema tutorial https://www.w3.org/2007/02/turtle/primer/#L3514
Based on the RDF Schema notes from the Primer - the following indicates hasVariant’s subject must be an instance satisfying all of the listed Abundances rather that one of the listed Abundances. It also indicates that the RDF Schema’s functionality is based on how it is used. So @abargnesi - would you rather have the listed options as below or just list bel:Abundance even though CompositeAbundance can’t be used with hasVariant?
belv:hasVariant rdf:type rdf:Property ;
    rdfs:domain belv:GeneAbundance ;
    rdfs:domain belv:RNAAbundance ;
    rdfs:domain belv:MicroRNAAbundance ;
    rdfs:domain belv:ProteinAbundance .
Nick Bargnesi
@nbargnesi
@abargnesi I'd like to get your feedback on nbargnesi/bel-parser@2df027c when possible
basic complete/incomplete AST generation for Identifiers
Tony Bargnesi
@abargnesi
@nbargnesi Ok! I reviewed things at nbargnesi/bel-parser@2df027c
I need to enable gitter reporting for bel_parser, will do that now.
Ok, github activity enabled on chat for bel_parser.
Tony Bargnesi
@abargnesi
@nbargnesi if you get the chance, test out https://reviewable.io for code reviews. You can test out without authorization to your organization, which is great. The interface is pretty busy, but it has some nice features. (1) You can review and add a whole bunch and then Publish it as one "review" instead of a bunch of little comments. (2) Diff editor mixes comments with code fairly nicely. (3) Comment resolution status which seems like an interesting way to democracize.
Still can't attach a patch file to a comment.
GitHub isn't bad for now though
juliakozlovsky
@juliakozlovsky
Hi Folks - we (the ThomsonReuters team) have been reviewing the current status of BEL systems (taking a look at open issues in GIT, reviewing the old roadmap, etc.), to better understand how everything fits together, and what our potential future contributions/role can be. We could use a bit of help with the review, as our previous work has been mostly focused on the RDF modeling part. Would anyone be available in the next couple of weeks to chat with us for an hour or so? We can do a webex, or grab a lunch somewhere convenient..
Dexter Pratt
@dexterpratt
Hi Julia, this is very timely for me and the NDEx project. I would love to talk. Several things are going on here. First, I've volunteered UCSD to take over the hosting of BEL web sites (Trey Ideker is on board with this). Second, Tony and I are actively discussing BEL<->CX conversion that will make BEL flow more easily in and out of the Cytoscape + NDEx world. Third, with respect to TR, we have started a design discussion for the next version of the NDEx R client where Alex Ishkin was the major contributor to the first version and is actively engaged in the discussion. This third point connects to BEL in that I want to make sure that NDEx <-> CX <-> R works well for BEL.
juliakozlovsky
@juliakozlovsky
@dexterpratt Hi Dexter - sounds great, I'll send a calendar request
Charles Tapley Hoyt
@cthoyt
Question: what is the meaning of a statement like translocation(proteinAbundance(PFH:"DVL Family"),MESHCL:Cytoplasm,MESHCL:"Cell Membrane") increases complexAbundance(proteinAbundance(PFH:"DVL Family"),proteinAbundance(PFH:"DVL Family"))where the same entity appears twice in a complex? Is this even allowed? For context, see line 2558 of the Selventa Small Corpus v1.0 (http://resources.openbel.org/belframework/1.0/knowledge/small_corpus.bel)
William Hayes
@wshayes
@cthoyt Translocation of ‘DVL Family’ proteins to Cell Membrane increases complex formation of ‘DVL Family’ proteins. We don’t restrict entering the same entity multiple times in a complex - an entity can bind to itself multiple times to form a complex, but I don’t believe it’s considered best practice (remember the BEL content made available was built over many years - we are hoping to build a deprecation/warnings engine to help refine and update some of these BEL statements).
berenicew
@berenicew
Hi,
I used the bel2rdf converter. It's seems that there is an issue when calling namespace related values. The converter works perfectly for small_corpus for example, but it's returning an error for large_corpus. I did some check and it's when I SET a value with a reference to a namespace that the error happened. Any idea how to fix or turn around the issue. (I created a github issue Error bel2rdf #130). Best regards, Bere,oce
Berenice
berenicew
@berenicew
Question : What is the purpose of group statement?
stianSjoli
@stianSjoli
Dear someone, I am new to openBEL, but see that it might be smart to use for a project that I am involved with. I see that there are different parsers of the BEL statements in the source code, but I wondered 1) where can I find the biggest source of curated biological BEL statements? 2) can someone recommend me some good tutorials of processing these statements?
Charles Tapley Hoyt
@cthoyt
@stianSjoli there are example documents released from OpenBEL at http://resources.openbel.org/belframework/20150611/knowledge/. The examples are various sizes, with the Large Corpus being significantly larger than the rest. http://resources.openbel.org/belframework/20150611/ also contains folders for the annotations and namespaces that have been released by OpenBEL. We're actively developing a parser at http://pybel.readthedocs.io/ and suite of tools to analyze BEL networks at http://pybel-tools.readthedocs.io
chris-ntua
@chris-ntua
Hello everyone , i'm new to openBEL and I have a problem trying to compile a KAM. The problem seems to be with the URL i'm using and the compiler can't download the needed resources. I'm using www.resource.belframework.org as the default one listed in the config file but I get an error that the download is not possible. I tried changing the URL in the config file to https://resources.openbel.org/belframework/20150611/index.xml but it still doesn't work. After some searching I came across a troubleshooting page in the wiki and it seems that one solution is to configure the proxy https://wiki.openbel.org/display/BFT , but I don't know how to go on about doing that and I'd really appreciate if you could help me out. Thanks a lot.