News & Events

Updated 'curated' datasets (13 March 2017)

Updated data models

FaceBase has made a major upgrade of the underlying database schema for the Data Browser. What this means to users is that moving forward, our new data will provide far more details to help you discover data in new ways. Note that as a result, the URL schema of data records has changed and older bookmarks to datasets will no longer work.

Updated processing

The new data model requires more extensive curation of the data. To accelerate access of data to the community, we will provide access to minimally curated data sets as soon as we can after they’re submitted.

Then, after a round of careful curation, we will update the datasets on the website and change their status to ‘Curated’.

Newly curated datasets

Our first set of finely curated datasets are the ones we released last month.

• Transgenic Mouse Enhancer OPT Assays - ChIP-seq, RNA-seq and transgenic assays to identify non-coding regulatory elements (enhancers) active during craniofacial development from the Genomic and Transgenic Resources for Craniofacial Enhancer Studies project.

• Alk5 Control – Bone and Soft Tissue microCT images (from E16.5 to P0) from the Integrated research of functional genomics and craniofacial morphogenesis project

• Wild Type E18.5 Frontal Suture Images from the Transcriptome Atlases of the Craniofacial Sutures project.

2017 FaceBase Annual Meeting in Boston May 1-2 (03 March 2017)

The next annual meeting of the FaceBase Consortium will be held May 1-2 in Boston, MA. We are pleased to announce that once again, the first day of the meeting – Monday, May 1st – will be open to the general craniofacial research community and will be webcast.

During this day-long meeting, each FaceBase project will introduce themselves and describe their progress during the past year for FaceBase 2.

You can view the event page with details including how to register to attend the public portion here: 2017 FaceBase Annual Meeting.

(If you are a member of the FaceBase consortium, please contact help@facebase.org if you need help with internal registration/information.)

To attend the public portion of the meeting, please click this link to register.

Almost 30 New Datasets Released (02 February 2017)

We’re kicking off 2017 with some more new datasets from FaceBase 2 projects as well as integration of gene summary information within datasets.

New Datasets

We are pleased to offer 27 new datasets from FaceBase2 projects providing new microCT images and genomic data:

• Transgenic Mouse Enhancer OPT Assays - ChIP-seq, RNA-seq and transgenic assays to identify non-coding regulatory elements (enhancers) active during craniofacial development from the Genomic and Transgenic Resources for Craniofacial Enhancer Studies project.

• Alk5 Control – Bone and Soft Tissue microCT images (from E16.5 to P0) from the Integrated research of functional genomics and craniofacial morphogenesis project

• Wild Type E18.5 Frontal Suture Images from the Transcriptome Atlases of the Craniofacial Sutures project.

New Gene Summary integration

Where available, we have integrated gene summary information with the Data Browser. You can see our currently available summaries here. On details pages for a dataset where there is a gene summary available, a “Gene Summary” field appears with a link to the information.

Updated website navigation

We have tweaked the website navigation so that the first item, “Data Browser”, now offers the same search links displayed on the homepage, as well as links to the Gene Summary records available and a list of the new and pending datasets that have been or will soon be released. Links that used to be under “Data” but that were not part of the Data Browser have been moved under “Resources”.

If you have any questions or issues, please email help@facebase.org.

New OCDM Version 1.7.0 Just Released (30 January 2017)

We are happy to announce the latest release of the OCDM, version 1.7.0. Click to download the archive file:

http://sig.biostr.washington.edu/share/downloads/ocdm/release/latest/ocdm.zip

The work for this release focused on homology mappings between human and mouse developmental and postnatal anatomical entities in Craniofacial Human Mouse Mouse Ontology (CHMMO). Mappings include developmental entities, from the zygote to perinatal structures at progressive stages of development, with emphasis on embryonic precursors of components of musculoskeletal system of the head (muscles, bones, cartilages, skeletal ligaments and joints).

Provisional mappings were initially carried out based on similar or same names and then verified by our domain expert. We likewise consulted the literature for homology evidence, either based on direct molecular studies or inferred vertebrate Bauplan. Bi-directional one to one and uni-directional one to null mappings at the gross anatomical level were recorded in this work.

Sign up for a FaceBase account with existing credentials (19 October 2016)

The FaceBase Hub is implementing the final update to the authentication system for the FaceBase Data Browser to give new users the option to sign up for a FaceBase account using an existing ID (i.e., campus, NIH or Google logins) instead of needing to create yet another new account.

Note that our account management system is based on Globus Auth . These changes will allow us to take advantage of more options that Globus provides for logging in to FaceBase.

On Wednesday, October 19th, we will deploy an update to the account management software. As a result, when signing up for a FaceBase account, new users will be able to select one of the many supported identity providers (from InCommon and Google). This will create an account request which will be forwarded to the FaceBase Hub for approval.

All current users will still be able to use your existing FaceBase account using the “GlobusID” option. You may also link your current GlobusID to another trusted ID.

If you have any questions or issues, please email help@facebase.org .