Date   

HPO release 2021-10-10

Sebastian
 

Dear HPO Users,

we have used this Sunday to release the 2021-10-10 version of HPO and the HPO-association files. We have added 57 new HPO terms with a major focus on immunology. Please find a more detailed report at https://github.com/obophenotype/human-phenotype-ontology/blob/master/src/ontology/reports/hpodiff_hp_2021-08-02_to_hp_2021-10-10.xlsx.
As usual the new files are linked from:
- https://hpo.jax.org/app/download/ontology
- https://hpo.jax.org/app/download/annotation

We wish you a great start into the week and look forward to more suggestions to improve this resource.

Best wishes from the HPO team.


Suggestions for more detailed onset terms

Prof. Dr. Peter Robinson
 

Dear HPO community,
we have received a request to add subterms for "young adult onset". Different communities tend to use different cutoffs, and so I was wondering if there are any comments or suggestions about the ones proposed in this issue (which look quite reasonable to me):
https://github.com/obophenotype/human-phenotype-ontology/issues/7153
Also, we are planning to similarly add more granularity for prenatal onset terms and are looking for feedback.
thanks !
-Peter


HPO-related job offers in the Robinson lab

Prof. Dr. Peter Robinson
 

The Robinson lab at the Jackson Laboratory (JAX) invites applications for
--
Software Engineer
-- Bioinformatician
-- Postdoctoral associate
-- Biocurator

...to join a highly interactive, supportive, and interdisciplinary group of faculty, staff scientists, postdoctoral fellows, and students and enjoy access to state-of-the-art equipment and facilities at the The
Jackson Laboratory for Genomic Medicine in Farmington, CT. Peter Robinson is one of three principal investigators (PIs) of the Monarch Initiative, an integrative data and analytic platform connecting phenotypes to genotypes across species and is a member of the the JAX Center for Precision Genetics, contributing bioinformatic resources to support research employing genetically well-defined laboratory mice. 

The Software Engineer will play an important role in advancing the mission of the Robinson lab, which focuses on developing algorithms, ontologies, and software to advance research and support medical practice. The Robinson lab leads the development of the Human Phenotype Ontology (HPO), which has become the international standard for computational phenotype analysis in Mendelian disease and other areas. The lab has recently spearheaded the development of the Medical Action Ontology (MAxO), which intends to provide a computational foundation for searching and analyzing treatments and other medical management with a focus on genetic disease. The lab develops software for phenotype (HPO) driven diagnostics including the Phenomizer and LIRICAL. We develop graph algorithms including the first use of random-walk analysis for disease gene prediction, which was cited over 1000 times (Walking the interactome...). We have developed machine-learning and statistical approaches towards predicting pathogenicity of variants in exome or genome sequencing, including Genomiser and SQUIRLS. We develop software for the analysis of genomic data including ChIP-seq, which applies a novel saturation-based algorithm and RNA-seq, which uses a hierarchical Bayesian network to simultaneously assess gene expression and alternative splicing. Our Exomiser software is widely used by projects such as the 100,000 Genomes project to assess diagnostic exome and genome data. Peter Robinson leads the machine learning subgroup of the National COVID Cohort Collaborative (N3C), and recent projects have included the application of machine learning to EHR data of COVID-19 patients.

Our lab strives to be a welcoming and supportive environment where people of all backgrounds have the opportunity to develop algorithms and software at the cutting edge of translational bioinformatics. Lab members typically focus on one or two areas of interest in fields such as ontologies, semantic algorithms, or machine learning. We provide extensive on-the-job training in algorithms and software engineering as needed for the projects. 

Expectations

As a rule, we have learned about algorithms during the projects and so we do not expect candidates to come to us with knowledge of the above mentioned topics, but we do expect a strong interest in ontologies or algorithms and a desire to create good software. The candidate would be expected to contribute to a diverse portfolio of research undertaken by the lab. The Robinson lab is very collaborative, taking a team science approach to many projects and participating in efforts such as the Global Alliance for Genomics and Health (GA4GH). We expect the candidate to participate in collaborations, which means concretely participating in virtual conferences and co-developing code using GitHub. Other duties include contributing to publications, submission of grants and funding applications, potential commercialization opportunities, as well as partnerships and collaborations with the community-wide efforts aimed at promoting open, integrated, and rigorous practices in research and scholarly communication. This position may be eligible for remote or remote/office flex work.

The Robinson lab develops software mainly in Java and Python but works with a range of other technologies such as SQL, JavaScript, C++, Rust, and R.

Please contact Peter with questions or go to the following links

Postdoc -

https://thejacksonlaboratory.wd1.myworkdayjobs.com/External_JAX/job/Farmington-Connecticut/Postdoctoral-Associate---Bioinformatics_JR000362

 

 

Bioinformatician -

https://thejacksonlaboratory.wd1.myworkdayjobs.com/External_JAX/job/Farmington-Connecticut/Bioinformatician-I-II-III_JR000396

 

 

Software Engineer – to be reposted shortly (please contact Peter).

 

Scientific Curator -

https://thejacksonlaboratory.wd1.myworkdayjobs.com/External_JAX/job/Farmington-Connecticut/Scientific-Curator_JR000398




August 2021 release of HPO

Sebastian
 

Dear HPO contributors and users,

we have now release the August 2021 version of HPO. Besides other work, we have added ~100 terms for renal pathology in collaboration with Dr Avi Rosenberg and others of the Kidney Precision Medicine Program. In total we added 178 new HPO terms/classes.
Peter R. has also finalized the conversion of OMIM labels to a shorter and better readable format. We also corrected about 100 diseases to use the latest OMIM identifier.
The summary of changes in HPO is available at https://github.com/obophenotype/human-phenotype-ontology/blob/master/src/ontology/reports/hpodiff_hp_2021-06-13_to_hp_2021-08-02.xlsx

The HPO team wishes you all a nice summer. Thank you for your continued support.

Best,
Sebastian, on behalf of the HPO consortium.


Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity

Prof. Dr. Peter Robinson
 

Dear friends of the HPO!

This article will be of interest for anybody using HPO to annotate or analyze immunological disease:
https://www.jacionline.org/article/S0091-6749(21)00732-6/fulltext

best wishes, Peter


HPO release June 2021

Sebastian
 

Dear HPO Users,

we have released a new version of HPO for June 2021 (2021-06-08). The key changes are:
• 191 new HPO terms
• Almost 100 changes to primary labels
• Almost 500 synonym changes

HPOA (the disease and gene annotations) has also been updated to reflect the latest changes and additions.

A more comprehensive list of changes of HPO can be found here: https://github.com/obophenotype/human-phenotype-ontology/blob/master/src/ontology/reports/hpodiff_hp_2021-04-13_to_hp_2021-06-08.xlsx

Thanks a lot for your constant support and input.

Best wishes,
Your HPO team


Modeling seizures in the Human Phenotype Ontology according to contemporary ILAE concepts makes big phenotypic data tractable

Prof. Dr. Peter Robinson
 

Hi everybody,
I'd like to point out a new article about collaborative work we have done the authors of this publication to improve the coverage of HPO for seizure phenotypes.
https://pubmed.ncbi.nlm.nih.gov/33949685/
-Peter


Phenopackets version 2 is open for comment.

Prof. Dr. Peter Robinson
 

Dear everybody,
the HPO team has been involved in the development of the Global Alliance for Genomics and Health (GA4GH) Phenopacket standard. Phenopackets can be used to report patient phenotypes using HPO and essentially provide additional context and can also be used as input format for tools that use HPO such as Exomiser.

We would welcome feedback via GA4GH:
Phenopackets v2.0 is now open for comment. Please submit comments and feedback via GitHub or email by Thursday, May 27 at 5pm GMT.
https://www.ga4gh.org/

Here is the documentation for v2:
https://phenopackets-schema.readthedocs.io/en/v2/

best wishes, Peter Robinson


April 2021 release

Sebastian
 

Dear HPO Users,

the April 2021 release of HPO and HPOA (disease/gene annotations) is now available at:

https://hpo.jax.org/app/download/ontology
and
https://hpo.jax.org/app/download/annotation

57 HPO classes were added from multiple areas with a focus on terms for pulmonology and COVID-19. Further changes are reported as usual in this excel-sheet: https://github.com/obophenotype/human-phenotype-ontology/blob/master/src/ontology/reports/hpodiff_hp_2021-02-28_to_hp_2021-04-13.xlsx

Please keep on adding suggestions for improvements to our issue-tracker at https://github.com/obophenotype/human-phenotype-ontology/issues.

Thanks,
Sebastian, on behalf of the HPO community.


Locations of HPO download files

Prof. Dr. Peter Robinson
 

Dear everybody,
a few of the HPO project download files have moved. Please make sure you are using the persistent uniform resource locators (PURLs) as noted here:

https://hpo.jax.org/app/download/ontology
https://hpo.jax.org/app/download/annotation

The PURLs redirect to whatever the current "real" location is.
best wishes, Peter & Seb


February 2021 release

Sebastian
 

Dear HPO community,

we have just published a new version of the Human Phenotype Ontology and the HPO-annotation (HPOA) data.

In HPO we have added 279 new terms and obsoleted 5 terms. More details on the changes are here: https://github.com/obophenotype/human-phenotype-ontology/blob/master/src/ontology/reports/hpodiff_hp_2020-12-07_to_hp_2021-02-08.xlsx

Please note that due to unforeseen circumstances the URLs where HPOAs were previously made available (compbio.charite.de/jenkins) will not be working anymore soon and we have moved everything to servers from the monarch-initiative. Please always use the PURLs (permanent URLs) for HPO and HPOAs, which we list here: https://hpo.jax.org/app/download/annotation

Best wishes,
the HPO team


The Human Phenotype Ontology in 2021

Prof. Dr. Peter Robinson
 

Hi everybody,
here is a recent update from the HPO:
Köhler S, et al. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D1207-D1217.
https://pubmed.ncbi.nlm.nih.gov/33264411/

best wishes, Peter


December 2020 release

Sebastian
 

Dear HPO community,

we are happy to announce the December 2020 release of the HPO and the disease annotation files. We have introduced 147 new HPO terms with a focus on immunology, pulmonology, kidney precision medicine, and epilepsy.

A comprehensive list of changes can be found at: https://github.com/obophenotype/human-phenotype-ontology/raw/master/src/ontology/reports/hpodiff_hp_2020-10-12_to_hp_2020-12-07.xlsx

Thanks again for all the support and input.

Our warmest wishes for a happy holiday season,
The HPO team

P.S.: the latest HPO publication has just been released at https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa1043/6017351


Prenatal Human Phenotype Ontology (HPO) Working Group,

Prof. Dr. Peter Robinson
 

Dear Colleagues, 
 

You are formally invited to participate in the Prenatal Human Phenotype Ontology (HPO) Working Group, led by Dr. Peter Robinson and Dr. Ronald Wapner with the support of the Fetal Sequencing Consortium. Given your expertise, we would like to include you in this project and hope you will be interested in participating in the prenatal ultrasound, MRI, echocardiogram, or pathology sub-group.   

Why are we doing this? 

The identification and evaluation of fetal structural anomalies is a major part of our practices.  Over the past few years, exome and now genome sequencing have demonstrated their importance in both the prenatal and neonatal management of these pregnancies.  Sequencing, however, is still early in transitioning into clinical care and we still have much to learn.  One of the critical steps in this transition is accurate phenotype-genotype correlation.  To accomplish this, we need standardized descriptions of fetal findings; both to make accurate clinical correlations and to incorporate emerging fields such as artificial intelligence into our interpretive tools. Use of the Human Phenotype Ontology has become the predominant approach to accomplishing this. 

What is HPO? 

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. A diagram of the HPO phenotyping process is attached below 

What is the goal of the Prenatal Human Phenotype Ontology (HPO) Working Group? 

Currently, the HPO does not have sufficient coverage of prenatal diseases or phenotypes. In order to develop this for our field, we need the input from experts and thought leaders to extend the ontology to include and define terms required to cover prenatal phenotypes allowing the linkage of typical imaging findings to corresponding HPO terms. Participants in this project will include ultrasonologists, echocardiologists, fetal MRI experts, and perinatal pathologists.   

We are seeking your expertise to support the expansion of HPO to prenatal phenotypes, which is essential to the further development and use of exome/genome sequencing in prenatal research and clinical practice. 

What is the time commitment? 

Attendance at one orientation (2 hours) and then bi-weekly meetings with your working group (2 hours per month). You will be tasked with reviewing literature and adjudicating with your colleagues regarding appropriate terminology use and classification  

Are there sub-specialty working groups? 

Yes, there will be separate groups reviewing phenotypes seen via fetal ultrasound, MRI, echocardiogram, and pathology.  Please let us know in your registration the area you are interested in.

How do I participate? 

To confirm your interest, please register for the working group here. You are encouraged to register if you want to be included on this mailing list moving forward.

To accommodate participants from multiple countries and time zones, we will host two orientation/kick off calls on Monday 12/14: 8:30a-10:30a EST and Wednesday 12/16 5-7pm EST. Please register for the one that best fits your schedule. 

Although a recording will be made available of the orientation, you are encouraged to attend a synchronous event. Once completing the orientation/kickoff, working groups will meet regularly with the experts within your team. The coordination of the bi-weekly effort will be overseen by Dr. Robinson, Dr. Wapner, and Jessica Giordano.  

Workshop Orientation Option 1 Monday 12/14: 8:30am-10:30am EST: Register here

Workshop Orientation Option 2 Wednesday 12/16 5-7pm EST: Register here.

Please reach out to Jessica Giordano if you have any questions and forward to colleagues/fellows who may be interested. It is possible we have missed folks essential to this work due to lack of email or awareness of an individual's interest. Thank you for your interest and support of this exciting and transformative work. 

Best, 

Dr. Ronald Wapner 

Dr. Peter Robinson 

Jessica Giordano, MS, CGC


October 2020 release of HPO

Sebastian
 

Dear HPO users,

we are happy to announce our October 2020 release of HPO.

We have added 126 new HPO terms - mostly abnormal concentrations of chemicals and several terms from pulmonology.

A more comprehensive list of changes can be found here: https://github.com/obophenotype/human-phenotype-ontology/raw/master/src/ontology/reports/hpodiff_hp_2020-08-11_to_hp_2020-10-12.xlsx

Thanks a lot for all the support and input.

Best wishes,
Sebastian, on behalf of the HPO team


HPO release - August 2020

Sebastian
 

Dear HPO-community,

two months are over and we have created the HPO release for August 2020.

We have again added almost 200 new HPO classes. This release has a special focus on laboratory abnormalities and bone fractures.

We provide diff-reports as xls, in case you want to have a detailed view on the changes: https://github.com/obophenotype/human-phenotype-ontology/tree/master/src/ontology/reports

Let us know if you have questions.

All the best,
Sebastian (on behalf of the HPO team)


--
Dr. Sebastian Köhler
Information Architect @ Ada Health
Member of Monarch Initiative


June 2020 release of HPO

Sebastian
 

Dear HPO Users,

we have just created a new HPO release for June 2020.

We have added 103 new classes, mostly from pulmonological diseases. Besides that we have restructured the hierarchies around
- pain
- seizures
- sexual dysfunctions

A more detailed report is available here: https://github.com/obophenotype/human-phenotype-ontology/blob/master/src/ontology/reports/hpodiff_hp_2020-03-27_to_hp_2020-06-08.xlsx?raw=true

Best,
Sebastian & the HPO team


March 2020 release aka the Epilepsome release

Sebastian
 

Hi HPO-fans,

we have just create a new HPO release with lots of new terms for better representation of epilepsy phenotypes (see Epilepsome project, further questions Peter Robinson or Ingo Helbig). Additionally, we fixed a few bugs and created many new logical definitions.

We also provide diff-reports as xls, in case you want to have a look at some changes: https://github.com/obophenotype/human-phenotype-ontology/tree/master/src/ontology/reports

Let me know if you have questions.

Stay safe wherever you are.

Best,
Seb (for HPO team)


February 2020 release aka "rare disease day release"

Sebastian
 

Dear HPO Users,

after November 2019, we finally provide the first HPO release in 2020. This new release introduces 129 new HPO terms (especially for the Kidney Precision Medicine Project and the Epilepsiome project), 45 updates of primary labels, over 600 changes to synonyms, 48 changed/added text-definitions. We have added lots of new British language synonyms (see https://github.com/obophenotype/human-phenotype-ontology/issues/5103)
The release also contains updates of several disease-HPO association files.

We also made major changes in the release files that link HPO terms to other entities, such as disease or genes. If you use these files please be aware of these changes, as they might break software that consumes these artifacts.
The file phenotype_annotation.tab now has a header line to make it easier to understand what each column contains. Also, there is an additional column (at the end) that contains the “sex-restriction”.

We previously had two build-jobs “hpo.annotation” and “hpo.annotation.monthly”. these have been merged into one with the name “hpo.annotation”. The number of files produced for gene-HPO associations has been significantly reduced, but the one file that is retained now contains more information. That means that the information of the files that were previously named:

• ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt
• ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt
• ALL_SOURCES_ALL_FREQUENCIES_phenotype_to_genes.txt
• ALL_SOURCES_FREQUENT_FEATURES_diseases_to_genes_to_phenotypes.txt
• ALL_SOURCES_FREQUENT_FEATURES_genes_to_phenotype.txt
• ALL_SOURCES_FREQUENT_FEATURES_phenotype_to_genes.txt
• OMIM_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt
• OMIM_ALL_FREQUENCIES_genes_to_phenotype.txt
• OMIM_ALL_FREQUENCIES_phenotype_to_genes.txt
• OMIM_FREQUENT_FEATURES_diseases_to_genes_to_phenotypes.txt
• OMIM_FREQUENT_FEATURES_genes_to_phenotype.txt
• OMIM_FREQUENT_FEATURES_phenotype_to_genes.txt
• ORPHA_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt
• ORPHA_ALL_FREQUENCIES_genes_to_phenotype.txt
• ORPHA_ALL_FREQUENCIES_phenotype_to_genes.txt
• ORPHA_FREQUENT_FEATURES_diseases_to_genes_to_phenotypes.txt
• ORPHA_FREQUENT_FEATURES_genes_to_phenotype.txt
• ORPHA_FREQUENT_FEATURES_phenotype_to_genes.txt


is now contained in the files:
• genes_to_phenotype.txt
• phenotype_to_genes.txt

The format is explained in the header of each file.


The file negative_phenotype_annotation.tab has been renamed to phenotype_annotation_negated.tab for consistency reasons.

If you have questions or suggestions, please contact us or file a ticket on our GitHub page (https://github.com/obophenotype/human-phenotype-ontology/issues).

Thank you very much for your support,
Sebastian, on behalf of the whole HPO community.

P.S.: Please also note that https://www.rarediseaseday.org/ is happening on February 29th.


Request for letter of support for HPO

Prof. Dr. Peter Robinson
 

Dear colleagues,

the HPO is planning to submit two NIH grant proposals to support our work and it would be extremely useful if members of this list could send us letters of support. I am now asking for support for our NHGRI U24 application (and will send another email in two weeks about a second proposal). The purpose of the U24 is to deepen the coverage of the HPO for more areas of medicine (e.g., neurology, immunology, pharmacogenomics,...). This will mean both adding new terms as well as new annotations (the annotations are the associations of HPO terms with diseases, e.g., here for Robinow syndrome: https://hpo.jax.org/app/browse/disease/OMIM:268310).

We will be requesting support for additional biocuration staff and also will be developing a Web-based collaboration portal through which collaborators can submit new terms or annotation data.

It would be extremely helpful to get letters of support that say

<We strongly support your proposal>
<As you know, our group does X>
<Our group currently uses HPO to do Y>
<Your proposal to develop a Web-based collaboration portal is extremely useful to us. We would contribute terms and annotations for our area of expertise, namely ABC>
<anything else>

We are also planning to conduct in person workshops for areas of medicine that require substantial additional terms. For instance, in 2018 we had an ophthalmology workshop that resulted in over 500 new HPO terms for the eye. If you feel that your area would benefit from such a workshop, please contact me, and I will send you a separate template letter of support.

thanks a lot in advance, Peter (peter.robinson@...) and Melissa (melissa@...), and in name of Sebastian Köhler, and Chris Mungal

Here is an example letter:

January 00, 2020


Peter Robinson, MD, MS

Jackson Laboratory of Genomic Medicine


Melissa Haendel, PhD

Oregon State University


Dear Peter and Melissa,

I am very excited about your NHGRI application, “The Human Phenotype Ontology: Accelerating Computational Integration of Clinical Data for Genomics.” 

As you know, I have been an active <contributor/user> of the Human Phenotype Ontology (HPO) for many years. Specifically, our group leverages the HPO for <XXX>

We could not be more grateful for your longstanding efforts to help standardize phenotype data, and could not accomplish our goals of <YYY> without the HPO. 

The HPO has organized productive collaborative workshops with clinical groups such as ours, that have aimed to revise and extend entire areas of the HPO (for example, see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324074/). The community then follows up with term requests, corrections, etc. by email and on our tracker.  We are delighted to hear about the new proposal to develop an online portal that will simplify our process of adding knowledge to the HPO database by allowing external collaborators such as ourselves to recommend annotations of HPO terms that describe a disease and then have the community and the HPO team be able to review and discuss them. We will be happy to add data and knowledge about <ADD YOUR AREA OF EXPERTISE HERE>



In summary, would be delighted to continue to provide feedback to the HPO team in the future on the HPO, disease annotations, and algorithms and tools that you all have been so dedicated at advancing. 

With the best of luck on your proposal, 

XXX

Name

Institution

Email








Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
860.837.2095 t | peter.robinson@... | https://robinsongroup.github.io/
Peter Robinson
---

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