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vfb's Introduction

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About Virtual Fly Brain

Virtual Fly Brain (VFB) is the only resource that integrates knowledge and images from across the field of Drosophila neurobiology. Our content is curated from the literature and from multiple bulk datasets: we have anatomical content from 100s of papers and expression & phenotype content from 1000s of papers; bulk image and expression data sets include data from flycircuit, Janelia Farm, Braintrap and the Labs of Kei Ito & Tzumin Lee. We believe it is essential for users to be able to trace assertions and data on our site back to thier origins in the literature and bulk data sets, and so are fanatical about retaining and displaying provenance for all our content.

Our underlying datamodel uses an OWL ontology of Drosophila anatomy featuring extensively referenced descriptions of hundreds of neuroanatomical structures and thousands of neuron classes. It also features an extensive collection of synonyms, which id used to drive our autocomplete-based text searches. An innovative logical component of this ontology drives all queries on the site. Queries for expression and phenotype have a second leg that directly queries FlyBase, to which all results are linked. Queries for images also make use of an OWL knowledge base that codifies the results of image analysis.

VFB also features an image stack browser displaying images of the adult brain, with segmentation following the BrainName standard, and the abdominal thoracic ganglion (in prep). Individual neuropil domains are painted and linked directly to terms in the anatomy ontology. Thousands of images registered to our standard stack are linked directly to our ontology and can be viewed directly in the stack browser.

We also provide extra analysis of single neuron image data via clustering of morphologically similar neurons using neuron blast software developed by Greg Jefferis & colleagues (manuscript in prep). Clustering finds many known classes as well as predicting new ones. Clusters can be viewed as rotatable 3D images.

Simple guide to editing this Repo

See the Code Editing Guide wiki.

Current issues that need work: Stories in Ready

Call for contributions

VFB is an open source project, increasingly embedded in the community it serves. We believe that VFB can only achieve its full potential - as a site integrated with and responsive to the community it serves - by tapping the expertise of its increasingly technically savvy user community.

We welcome all offers of contribution -

  • Are you a biologist who would like to improve or extend the existing biological content of the site?
  • Are you a VFB user willing to contribute critiques, user stories and feature requests?
  • Do you have good communications skills that you could use to report news about VFB or to make video tutorials?
  • Do you have an eye for design and think you could improve the look and feel of the site?
  • Do you have skills in image analysis or display that you could contribute?
  • Are you a coder with experience in javascript, python, java or JVM languages such as groovy or scala?
  • Do you have an interest in semantics and experience with OWL?

If you'd like to contribute please email our google group at vfb_community {at} googlegroups.com with details of your brackground and how you might be able to help out.

Social media presence

  • We are @virtualflybrain on twitter. Our feed features papers and news of general interest to the Fly Neuro community, as well as specific news about VFB.
  • Our blog lives here
  • We also have a page on FaceBook

Publications

  1. Osumi-Sutherland D., Reeve S., Mungall C., Ruttenberg A. Neuhaus F, Jefferis G.S.X.E, Armstrong J.D. (2012) A strategy for building neuro-anatomy ontologies. Bioinformatics 28(9): 1262-1269.
  2. Milyaev N., Osumi-Sutherland D., Reeve S., Burton N., Baldock R.A., Armstrong J.D. (2012) The Virtual Fly Brain Browser and Query Interface. Bioinformatics 28(3): 411-415
  3. Costa M., Reeve S., Grumbling G., Osumi-Sutherland D., (2013) The Drosophila anatomy ontology. Journal of Biomedical Semantics 4:32

Annotating your own data using our system

We maintain a page on the Drosophila anatomy ontology wiki outlining the advantages of annotating your own data using our system and providing links to resources for doing so.

Documentation

Please note. This is a work in progress. Most documentation currently lives in a google doc. We are in the process of transferring it to this wiki.

Overall architecture of project

Left panel shows the current architecture. Right panel shows planned development.

Architure

vfb's People

Contributors

robbie1977 avatar dosumis avatar mmc46 avatar jefferis avatar gidili avatar nstaudt avatar katrinleinweber avatar waffle-iron avatar ajdm avatar

Stargazers

Amy Robinson Sterling avatar Aaron McKenna avatar Clare Pilgrim avatar Nico Matentzoglu avatar andzil avatar Smrutiranjan Sahu avatar Michael Schmuker avatar Daniel Münch avatar Zaki Mughal [sivoais] avatar Matteo Cantarelli avatar avatar Tushar Bihani avatar avatar avatar Andrew Straw avatar avatar

Watchers

avatar Zaki Mughal [sivoais] avatar avatar James Cloos avatar avatar avatar Nico Matentzoglu avatar David (Dudi) Deutsch avatar Alex Holmes avatar avatar

Forkers

robbie1977 jefferis jefferislab jgrybak gidili

vfb's Issues

Show me how links opening

currently they open as a full page without a header footer etc.

Do we want this if so I'll add header/footer or do we want them as pop-up screens?

Hyperlink related anatomy terms in anatomy term page

e.g. for this entry

http://www.virtualflybrain.org/site/tools/anatomy_finder/index.htm?id=FBbt:00004013&name=suboesophageal%2520ganglion%2520(synonym)

it would be great if relevant terms in the Definition and Comment sections were hyperlinked to their pages. e.g. in the text below

  • esophagus
  • adult gnathal ganglion
  • adult subesophageal zone
  • GNG
  • saddle
  • prow
  • adult cerebral ganglion

Definition: Region of the brain beneath the esophagus, consisting of the fused ganglia of the three gnathal segments.
Comment: In the adult, this is referred to as adult gnathal ganglion (GNG). The adult subesophageal zone comprises the GNG, the saddle and the prow (which is included in the adult cerebral ganglion) (BrainName).

Bug in CSV downloads

If you run multiple CSV downloads from annotation queries in separate tabs, the results get muddled - often all 3 flavours (gene, transgene, phenotype) produce the same download. Results pages look fine.

Tested in Chrome.

Updating tree and mask to latest JFRC FlyBrain

This is an umbrella ticket for finishing updated to compliance with FlyBrain paper and JFRC FlyBrain mask.

  1. Update tree.
    Background: The clickable tree on the stack browser page is generated from a pair of JSON files.
    Progress: Tree generation has been moved to the VFB_owl repo. Previous Java code used in tree gen should be considered deprecated. The aim of the new code is for this to be completely automated from the ontology using Jython/Brain/owltools scripting, with key information for this derived from the VFB (LMB) DB. So far we have tools for updating names and for basic tree manipulation. These are probably sufficient for a short term update, but some progress on completely automating by taking advantage of OWLtools graphing. This is only hard because we need to guarantee single inheritance.
  2. Update mask:
    Progress:
    (a) We are in the process of confirming permissions and licensing.
    (b) Mapping domains: stack id -> FBbt; stack id -> tree nodeId
    Old domain mapping spreadsheet here: https://docs.google.com/spreadsheet/ccc?key=0AmK8olNJT0Z7dFdNR0N2SUpGcGVfMDBjcGljUzFrYWc&usp=drive_web#gid=0
  3. Update BrainName abbv mappings in lmb_fc_mysql

Longer term - the domains should be individuals in the VFB knowledgeBase. Mask and tree JSON should store these IDs.

Add link to downloads for clone stacks - (hosted on LMB server)

We currently have no download links for Ito, Cachero & Lee clone stacks. These are already available on an LMB server. We should to add a general download link to all of these for now and work on specific download links from the stack pages themselves.

Query for adult antennal lobe only returns PN clusters

For some reason the query Neurons with some part in adult antennal lobe, clustered by shape only returns projection neurons and not local neurons or indeed other random neurons with parts in the AL. Maybe this has something to do that the PNs have been hand annotated for their antennal lobe glomerulus innervation. @dosumis ?

The LNs likely have no manual annotation.

Issue present on both main and dev server

http://www.virtualflybrain.org/do/cluster_list.html?action=cluster_found&id=FBbt:00007401

http://vfbdev.inf.ed.ac.uk/do/cluster_list.html?action=cluster_found&id=FBbt:00007401

Upgrade Google Analytics

update the account to latest version enabling monitoring of page events to better judge user experience.

Will have to wait till main server update as might cause problems with old site being monitored.

Switch to using openID's

The current user system is not really user friendly and ideally we want users to organically login on enabling user engagement throughout the site.
This would allow people to use their google etc login but still enabling restricted access for specified users if required - which is what the current system is mainly used for.

patch queues for different servers?

Hi @Robbie1977 ,

I'm no expert on this, but might it be useful to set up some kind of (versioned) patch queue system for the different dev-servers? I haven't disentangled the dev branches enough to figure out how simple the differences are and how much they have changed over time, but it does seem to me that there is quite a lot of git merge noise related to this. Sample of potentially relevant links,

http://stackoverflow.com/questions/5016862/whats-the-git-approach-to-publish-a-patch-queue
http://cpeterso.com/blog/02013/03/stacked-git-mercurial-style-patch-queues-for-git/
https://github.com/jwhitley/topgit

Greg.

Compress OWL files?

@dosumis would you be happy if I added owl files to the routine that compacts and splits up wlz files?

This would mean you didn't need to worry about the size of the file anymore.

All you'd have to do is just run the deploy/compress.sh before committing a new file as the owl file itself would be ignored by git just the compressed copy uploaded.

see the deploy/README.md

If you're happy I'll add all *.owl files to the routine?

Add IDs to all TermInfo

As title. We should also have documentation in multiple places (including the float over text) encouraging users to use these IDs when referring to content.

Add query for unclustered single neurons overlapping specified region

We can currently query for clusters whose exemplar neuron overlaps some specified region currently via the query menu option

Individual neurons
. with some part here

The OWL query for this is.
cluster that has_exemplar some (overlaps some ?X)

This is useful in that it massively cuts down the number of hits when querying from large brain regions. But this strategy misses cases where a neuron overlaps some specified region but the exemplar of the cluster it belongs to does not. This is especially problematic for small brain regions such a single glomeruli. There are a number of glomeruli for which we have mapped neurons but these cannot be found via queries on VFB.

The obvious solution is to add an additional query for individual neurons. The OWL for this couldn't be simpler:

neuron that overlaps some ?X

The new menu should have 2 options

Individual neurons
. with some part here (preclustered)
. with some part here (unclustered)

The results page for the unclustered query should follow the layout of pages for cluster members/individuals of some specified class, e.g.:

http://www.virtualflybrain.org/do/individual_list.html?action=neuron_found&id=VFB_00014475&region=VGlut-F-600026

Query results can crash browser

If ALL is selected then the browser will crash when for example 1001 results are returned.

I suggest setting the max value allowed to 100 rather than ALL?

Hyperlink references in anatomy term pages

e.g. for the FB anatomy term page, the comment includes a large number of references that could be linked up:

Comment: Each of the two neighboring slices (1-2, 3-4, 5-6, 7-8) are associated more closely because they receive small-field columnar neurons generated by the same neuroblasts, forming four groups on each side of the midline, from lateral to medial: segment pair W, X, Y and Z (Boyan and Williams et al., 2011; Ito and Awasaki, 2008). Six to eight layers have been identified, depending on the staining that is used (Hanesch et al., 1989; Young and Armstrong, 2010; Kahsai and Winther, 2011).

Not sure if this needs to start with dois in the OWL file.

Centre FlyCircuit images on brightest slice

From June 2013

Marta and I wrote something to calculate the brightest slice for each stack in the flycircuit set in response to Douglas' suggestion. Spreadsheet and summary histogram attached.

Also, I guess @Nestor, Robbie and perhaps Bill, I noticed for the first time that the woolz data in the vfb browser has 326 slices, not 218 like the JFRC2 template. I presume that the stack has been inflated 50% in Z by adding interpolated slices, rather than by changing the Z spacing, and that strikes me as an odd choice. Is there a reason?

Data here: https://gist.github.com/jefferis/9411291

Note that this is the current list of good_images, which excludes 3 images in that list (leaving 16129).

brightestslicesflycircuit

Add Ito half brain stack + choice of neuropil and tract masks

Available here: ftp://ftp.flybase.org/flybase/associated_files/InsectBrainNomenclature_RawData.zip

Worth displaying this half brain even without registered stacks for (a) the 3 colour stain & (b) tract mask (none is available for JFRC brain)

add male fruitless stacks

Only female ones have been added, because we didn't have the male and female terms in the ontology at the time.
Now that we do (mmc46 to check it's all ok) add the stacks to the site, and to the image downloads.

Add possibility to query for overlap in 2 or more neuropils

It would be good to have the option of querying for neurons that overlap X and Y.
This could be an option added on Query builder. At the moment the drop-down menu only lists synaptic/presynaptic/postsynaptic, so an option for overlap could be added.

Example of feedback from form

Info below is automatically added

Support info:
/site/vfb_site/home.htm
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_2) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/33.0.1750.152 Safari/537.36

Post link to BrainName supplement data on FB

We have permission to post links to the BrainName supplement on the FB FTP servers. Would be good to get this done ASAP. Makes sense to have a flat page for this, but perhaps also post link in stack info summary for standard brain stack? The latter should also have a download link for the new JFRC stack.

Fix inflated number of Z slices in main adult brain template

Split from a discussion started for feature request #45 since this is clearly a separate, and I think quite serious, bug.

As noted in June 2013:
I noticed for the first time that the woolz data in the vfb browser has 326 slices, not 218 like the JFRC2 template. I presume that the stack has been inflated 50% in Z by adding interpolated slices, rather than by changing the Z spacing, and that strikes me as an odd choice. Is there a reason?

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