life, science, semantics
ontology
small world, big data

ONTOLOGY 101

Some useful links for ontology development

ONTOLOGY - Having relationship is a complicated thing
My ONTOLOGY 101 lecture at the University of Michigan DCMB seminar
The Application Ontology
Why application ontology is gaining traction in the database management domain
OBO Ontology
The Open Biomedical Ontology - what, why, how
OLS
SEARCH - query OBO ontologies with the EBI Ontology Lookup Service
ZOOMA
ANNOTATE - mapping free text to ontology class with Zooma
Webulous
CREATE - turning data in Google sheet to ontology classes






Projects

I have developed and continued maintaining these ontologies

The Experimental Factor Ontology - Developed and maintained at the EMBL-EBI. EFO is an application ontology that links domain ontologies together. It is the semantic backbone of CTTV, ENCODE, GWAS Catalog, ArrayExpress, Atlas, and many more.

The Cell Line Ontology - a multi-continent collaboration to build an integrative cell line information resource. CLO was born as a Cell Line Knowledgebase (CLKB) in 2005.

The Ontology of Adverse Events - orginally known as AEO. OAE captures drug-adverse event temporal association based on the bodily pathologial process of the drug response

Some of those

The moments from here and there

Dr.Brian Athey, Dr.Deb Walker

and mom...

Dr.Francis Collins

looks to be some discussion

another me and Dr.Collins

The man of the Human Genome Project

Dr.Leroy Hood

of P4 Medicine

The thesis committee

on the day I defended

Dr.Hiroaki Kitano

if you remember Aibo...

About

A food aficionado cat lady who fell in love with science



  • siiraa!

    the gem head...

    Sirarat is the gem head in Sanskrit. The extra i and extra a are just there to confuse you. BSc Computer Science, Mahidol University International College. MS PhD Bioinformatics, University of Michigan. A Fulbright scholar. An ORISE fellow at FDA Office of Clinical Pharmacology. An ontologist at EMBL-EBI. ORCID: 0000-0002-2548-641X
    LinkedIn: tinyurl.com/sirarat

  • Food

    A serious hobby

  • The furry friends

    Please consider adopting

    Both of them were my sanity check at four in the morning during my thesis-writing period, whom I even thanked in my dissertation. Many thanks to Camp Kitty for their road tour to Ann Arbor Petco in June 2006. Some of the places to get you started on adopting a friend - Battersea, Woodgreen, ASPCA, and WARL. With all the thanks from my heart, Thank you.

  • #lifeisajourney

    From Bangkok to Saskatoon and back

    "Travel. As much as you can. As far as you can. As long as you can. Life's not meant to be lived in one place" --- unknown

    Then Saskatoon to Bangkok to Ann Arbor to Silver Spring to Cambridge... "Where are you from?" gets trickier to answer as life goes on, but never once had I regretted any of it.

    "Life is not meant to be lived in one place..."



Publications


Linking rare and common disease: mapping disease-phenotypes to ontologies in therapeutic target validation
Sarntivijai S, Vasant D, Saunders G, Bento P, Gonzalez D, Betts J, Hasan S, Koscielny G, Dunham I, Parkinson H, Malone J.
J Biomed Semantics. 2016 Mar 23;7:8. PMID: 27011785

Linking MedDRA®-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.
Sarntivijai S, Zhang S, Jagannathan DG, Zaman S, Burkhart KK, Omenn GS, He Y, Athey BD, Abernethy DR.
Drug Saf. 2016 Mar 22. PMID: 27003817

Use of internet search logs to evaluate potential drug adverse events
Sarntivijai, S, Abernethy DR
Clin Parmacol Ther. 2014 Aug;96(2):149-50. doi: 10.1038/clpt.2014.115. PMID: 25056395

CLO: The Cell Line Ontology.
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Sch├╝rer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y.
J Biomed Semantics. 2014 Aug 13;5:37. doi: 10.1186/2041-1480-5-37. eCollection 2014. PMID:25852852

Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines.
Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, He Y.
PLoS One. 2012;7(11):e49941. doi: 10.1371/journal.pone.0049941. Epub 2012 Nov 28. PMID: 23209624

A bioinformatics analysis of the cell line nomenclature.
Sarntivijai S, Ade AS, Athey BD, States DJ.
Bioinformatics. 2008 Dec 1;24(23):2760-6. doi: 10.1093/bioinformatics/btn502. Epub 2008 Oct 10. PMID: 18849319

For a complete list of publications, please see ResearchGate: Sirarat_Sarntivijai