This document discusses efforts to enhance accessibility of rare disease literature for researchers and patients. It describes adding layperson synonyms to the Human Phenotype Ontology to help patients understand disease descriptions. Over 44% of existing synonyms were marked as layperson terms. The document also discusses a pilot project to annotate rare disease case reports with associated genes and phenotypes to identify the rarest cases and facilitate information sharing and community building. Next steps include further literature annotation and incorporating the data into databases. The overall goal is to improve dissemination of information on rare diseases.
The Human Phenotype Ontology (HPO) was developed to describe phenotypic abnormalities, aka, “deep phenotyping”, whereby symptoms and characteristic phenotypic findings (a phenotypic profile) are captured. The HPO has been utilized to great success for assisting computational phenotype comparison against known diseases, other patients, and model organisms to support diagnosis of rare disease patients. Clinicians and geneticists create phenotypic profiles based on clinical evaluation, but this is time consuming and can miss important phenotypic features. Patients are sometimes the best source of information about their symptoms that might otherwise be missed in a clinical encounter. However, HPO primarily use medical terminology, which can be difficult for patients and their families to understand. To make the HPO accessible to patients, we systematically added non-expert terminology (i.e., layperson terms) synonyms. Using semantic similarity, patient-recorded phenotypic profiles can be evaluated against those created clinically for undiagnosed patients to determine the improvement gained from the patient-driven phenotyping, as well as how much the patient phenotyping narrows the diagnosis. This patient-centric HPO can be utilized by all: in patient-centered rare disease websites, in patient community platforms and registries, or even to post one’s hard-to-diagnosed phenotypic profile on the Web.
Data Translator: an Open Science Data Platform for Mechanistic Disease Discoverymhaendel
Architecture of language and data translation that underlays the NCATS Biomedical Data Translator. Presented at the Fanconi Anemia Annual Meeting. http://fanconi.org/index.php/research/annual_symposium
The Human Phenotype Ontology (HPO) was developed to describe phenotypic abnormalities, aka, “deep phenotyping”, whereby symptoms and characteristic phenotypic findings (a phenotypic profile) are captured. The HPO has been utilized to great success for assisting computational phenotype comparison against known diseases, other patients, and model organisms to support diagnosis of rare disease patients. Clinicians and geneticists create phenotypic profiles based on clinical evaluation, but this is time consuming and can miss important phenotypic features. Patients are sometimes the best source of information about their symptoms that might otherwise be missed in a clinical encounter. However, HPO primarily use medical terminology, which can be difficult for patients and their families to understand. To make the HPO accessible to patients, we systematically added non-expert terminology (i.e., layperson terms) synonyms. Using semantic similarity, patient-recorded phenotypic profiles can be evaluated against those created clinically for undiagnosed patients to determine the improvement gained from the patient-driven phenotyping, as well as how much the patient phenotyping narrows the diagnosis. This patient-centric HPO can be utilized by all: in patient-centered rare disease websites, in patient community platforms and registries, or even to post one’s hard-to-diagnosed phenotypic profile on the Web.
Data Translator: an Open Science Data Platform for Mechanistic Disease Discoverymhaendel
Architecture of language and data translation that underlays the NCATS Biomedical Data Translator. Presented at the Fanconi Anemia Annual Meeting. http://fanconi.org/index.php/research/annual_symposium
Human embryonic stem cell-derived retinal pigment epithelium in patients with age-related macular degeneration and Stargardt's macular dystrophy: follow-up of two open-label phase 1/2 studies
Published Online: 15 October 2014
Including Comment By, Anthony Atala
Lymphoma of the Tonsil in a Developing Communityasclepiuspdfs
The lymphoma of the tonsil is a rarity. Single case reports have appeared in countries as disparate as China, Greece, India, Japan, and Turkey. Therefore, this paper presents cases found in Nigeria among the Ibo ethnic group. The epidemiological comparisons are deemed to be worthy of documentation such as age ranges and sides of involvement.
Purpose: To characterize the clinical features of ocular toxoplasmosis (OT) in Central Cuba. Methods: A database at a large regional referral center was searched for patients who, from April 1, 2011 to May 31, 2013, had the potential diagnosis of OT. Inclusion criteria were the clinical diagnosis of OT, characterized by focal retinochoroidal inflammation. Medical records were reviewed to confirm inclusion criteria (visual acuity recorded in decimal form).
Results: 279 patients (329 total eyes) were affected with OT. Overall, 66.7% were diagnosed with acquired OT with a mean age of 35.4 years and 1.8% with congenital OT with a mean age of 3.4 years. The time of onset of OT could not be determined in 28.3% (n=79) of patients. Patient clinical presentations were posterior uveitis (72.8 %), quiescent retinochoroiditis (16.1 %), and panuveitis (11.1%). Fourteen percent of patients had a slight decrease (0.9-0.6) in visual acuity, 44.4% a moderate decrease (0.5-0.2), and 41.6% a marked decrease (< 0.1).
There is emerging use of alternate light sources (ALS) in the evaluation of child abuse, sexual assault and domestic violence cases. There are important evidence-based elements of this practice essential to understand before considering the tool "diagnostic" of bruising. There are bruise mimics, and skin substances and conditions that may "light up" (during the process of fluorescence - light absorption through emission) essential for the legal and medical professionals involved in forensic medical care to understand. With emerging practice in the SANE/SAFE community to use ALS to confirm "strangulation", this paper is a good tool to understand the sensitivity and specificity of this tool and use with proper and responsible practice. Study developed as a means to understand the sensitivity and specificity of ALS in this context.
Este estudio sostiene que existen al menos doce genes implicados en el color del pelo y que éstos presentan un total de 45 variaciones diferentes (polimorfismos de un solo nucleótido, SNP por sus siglas en inglés). Otros trabajos han confirmado que algunos genes controlan los diferentes matices, algunos le dan el color, otros el brillo, otros la tonalidad, otros lo hacen más oscuro o más claro, etc.
Empowering patients by increasing accessibility to clinical terminologyNicole Vasilevsky
Flash talk at Medical Library Association Pacific Northwest Chapter meeting in Portland, OR on October 18, 2016.
http://pnc-mla.cloverpad.org/annual2016
Authors: Erin Foster, Mark Engelstad, Chris Mungall, Peter Robinson, Sebastian Kohler, Melissa Haendel and Nicole Vasilevsky
Dr. Katherine Sims opens the Norrie Disease Association's first international conference with a warm welcome and historical overview of Norrie Disease. (NDA International Conference, 2009)
The Application of the Human Phenotype Ontology mhaendel
Presented at the II International Summer School for Rare Disease and Orphan Drug Registries, September 15-19, 2014, Organized by the National Centre for Rare Diseases
Istituto Superiore di Sanità (ISS), Rome, Italy.
Note the extensive contribution by many consortium members and partners listed in the acknowledgements slide.
Human embryonic stem cell-derived retinal pigment epithelium in patients with age-related macular degeneration and Stargardt's macular dystrophy: follow-up of two open-label phase 1/2 studies
Published Online: 15 October 2014
Including Comment By, Anthony Atala
Lymphoma of the Tonsil in a Developing Communityasclepiuspdfs
The lymphoma of the tonsil is a rarity. Single case reports have appeared in countries as disparate as China, Greece, India, Japan, and Turkey. Therefore, this paper presents cases found in Nigeria among the Ibo ethnic group. The epidemiological comparisons are deemed to be worthy of documentation such as age ranges and sides of involvement.
Purpose: To characterize the clinical features of ocular toxoplasmosis (OT) in Central Cuba. Methods: A database at a large regional referral center was searched for patients who, from April 1, 2011 to May 31, 2013, had the potential diagnosis of OT. Inclusion criteria were the clinical diagnosis of OT, characterized by focal retinochoroidal inflammation. Medical records were reviewed to confirm inclusion criteria (visual acuity recorded in decimal form).
Results: 279 patients (329 total eyes) were affected with OT. Overall, 66.7% were diagnosed with acquired OT with a mean age of 35.4 years and 1.8% with congenital OT with a mean age of 3.4 years. The time of onset of OT could not be determined in 28.3% (n=79) of patients. Patient clinical presentations were posterior uveitis (72.8 %), quiescent retinochoroiditis (16.1 %), and panuveitis (11.1%). Fourteen percent of patients had a slight decrease (0.9-0.6) in visual acuity, 44.4% a moderate decrease (0.5-0.2), and 41.6% a marked decrease (< 0.1).
There is emerging use of alternate light sources (ALS) in the evaluation of child abuse, sexual assault and domestic violence cases. There are important evidence-based elements of this practice essential to understand before considering the tool "diagnostic" of bruising. There are bruise mimics, and skin substances and conditions that may "light up" (during the process of fluorescence - light absorption through emission) essential for the legal and medical professionals involved in forensic medical care to understand. With emerging practice in the SANE/SAFE community to use ALS to confirm "strangulation", this paper is a good tool to understand the sensitivity and specificity of this tool and use with proper and responsible practice. Study developed as a means to understand the sensitivity and specificity of ALS in this context.
Este estudio sostiene que existen al menos doce genes implicados en el color del pelo y que éstos presentan un total de 45 variaciones diferentes (polimorfismos de un solo nucleótido, SNP por sus siglas en inglés). Otros trabajos han confirmado que algunos genes controlan los diferentes matices, algunos le dan el color, otros el brillo, otros la tonalidad, otros lo hacen más oscuro o más claro, etc.
Empowering patients by increasing accessibility to clinical terminologyNicole Vasilevsky
Flash talk at Medical Library Association Pacific Northwest Chapter meeting in Portland, OR on October 18, 2016.
http://pnc-mla.cloverpad.org/annual2016
Authors: Erin Foster, Mark Engelstad, Chris Mungall, Peter Robinson, Sebastian Kohler, Melissa Haendel and Nicole Vasilevsky
Dr. Katherine Sims opens the Norrie Disease Association's first international conference with a warm welcome and historical overview of Norrie Disease. (NDA International Conference, 2009)
The Application of the Human Phenotype Ontology mhaendel
Presented at the II International Summer School for Rare Disease and Orphan Drug Registries, September 15-19, 2014, Organized by the National Centre for Rare Diseases
Istituto Superiore di Sanità (ISS), Rome, Italy.
Note the extensive contribution by many consortium members and partners listed in the acknowledgements slide.
Supporting Genomics in the Practice of Medicine by Heidi RehmKnome_Inc
View the webinar at http://www.knome.com/webinar-supporting-genomics-practice-medicine. In this presentation, Dr. Heidi Rehm, Chief Laboratory Director of the Laboratory for Molecular Medicine at Partners Healthcare and one of the Principal Investigators on ClinGen, elucidates the challenges of genomics in medicine and outlined the path to integrating large scale sequencing into clinical practice.
Mucopolysaccharidosis type II MPS II or Hunter syndrome is Metabolism by lysosomal accumulation with a recessive inheritance pattern associated with the X chromosome. It is caused by lack of activity of the lysosomal enzyme iduronate 2 sulfatase, encoded by the IDS gene. Plasma iduronate 2 sulfatase enzymatic activity was measured and the IDS gene in genomic DNA was analyzed by automated direct sequencing. The enzyme activity was 1.2 mol l h reference value 2 mol l h and molecular analysis detected the mutation c.1403G A p.R468Q , confirming the diagnosis of MPS II. rice field. In conclusion, there are few groups dedicated to this disease family here in Mexico, highlighting the need to form an expert team of physicians and scientists dedicated to inborn errors of metabolism to stay up to date. Miss. Parimala L | Babu M "Hunter Syndrome: A Case Report" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-7 | Issue-1 , February 2023, URL: https://www.ijtsrd.com/papers/ijtsrd52814.pdf Paper URL: https://www.ijtsrd.com/medicine/other/52814/hunter-syndrome-a-case-report/miss-parimala-l
Discovery of new form of dystrophin protein could lead to therapy for some Duchenne muscular dystrophy patients
&
Genetics, lifestyle have a strong impact on biomarkers for inflammation, cancer
Similar to Enhancing Rare Disease Literature for Researchers and Patients (20)
Presentation given at the Indiana University School of Medicine's Ruth Lilly Medical Library. Contains information and resources specific to Indiana University Purdue University Indianapolis (IUPUI). For full class materials, see LYD17_IUPUIWorkshop folder here: https://osf.io/r8tht/.
Measuring competence: building an assessment tool for public health graduate ...Erin D. Foster
Presentation for the Pacific Northwest Region of the National Network of Libraries of Medicine "PNR Partners" webinar series in March 2016.
Link to webinar recording: https://www.youtube.com/watch?v=uaKc8Aa4Gko
Supporting Terminology Standards and Interoperability in Nursing PracticeErin D. Foster
Poster presentation at the Medical Library Association annual conference in May 2016.
Link to webpage: https://www.nlm.nih.gov/research/umls/Snomed/nursing_terminology_resources.html
Anti ulcer drugs and their Advance pharmacology ||
Anti-ulcer drugs are medications used to prevent and treat ulcers in the stomach and upper part of the small intestine (duodenal ulcers). These ulcers are often caused by an imbalance between stomach acid and the mucosal lining, which protects the stomach lining.
||Scope: Overview of various classes of anti-ulcer drugs, their mechanisms of action, indications, side effects, and clinical considerations.
New Directions in Targeted Therapeutic Approaches for Older Adults With Mantl...i3 Health
i3 Health is pleased to make the speaker slides from this activity available for use as a non-accredited self-study or teaching resource.
This slide deck presented by Dr. Kami Maddocks, Professor-Clinical in the Division of Hematology and
Associate Division Director for Ambulatory Operations
The Ohio State University Comprehensive Cancer Center, will provide insight into new directions in targeted therapeutic approaches for older adults with mantle cell lymphoma.
STATEMENT OF NEED
Mantle cell lymphoma (MCL) is a rare, aggressive B-cell non-Hodgkin lymphoma (NHL) accounting for 5% to 7% of all lymphomas. Its prognosis ranges from indolent disease that does not require treatment for years to very aggressive disease, which is associated with poor survival (Silkenstedt et al, 2021). Typically, MCL is diagnosed at advanced stage and in older patients who cannot tolerate intensive therapy (NCCN, 2022). Although recent advances have slightly increased remission rates, recurrence and relapse remain very common, leading to a median overall survival between 3 and 6 years (LLS, 2021). Though there are several effective options, progress is still needed towards establishing an accepted frontline approach for MCL (Castellino et al, 2022). Treatment selection and management of MCL are complicated by the heterogeneity of prognosis, advanced age and comorbidities of patients, and lack of an established standard approach for treatment, making it vital that clinicians be familiar with the latest research and advances in this area. In this activity chaired by Michael Wang, MD, Professor in the Department of Lymphoma & Myeloma at MD Anderson Cancer Center, expert faculty will discuss prognostic factors informing treatment, the promising results of recent trials in new therapeutic approaches, and the implications of treatment resistance in therapeutic selection for MCL.
Target Audience
Hematology/oncology fellows, attending faculty, and other health care professionals involved in the treatment of patients with mantle cell lymphoma (MCL).
Learning Objectives
1.) Identify clinical and biological prognostic factors that can guide treatment decision making for older adults with MCL
2.) Evaluate emerging data on targeted therapeutic approaches for treatment-naive and relapsed/refractory MCL and their applicability to older adults
3.) Assess mechanisms of resistance to targeted therapies for MCL and their implications for treatment selection
Title: Sense of Smell
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the primary categories of smells and the concept of odor blindness.
Explain the structure and location of the olfactory membrane and mucosa, including the types and roles of cells involved in olfaction.
Describe the pathway and mechanisms of olfactory signal transmission from the olfactory receptors to the brain.
Illustrate the biochemical cascade triggered by odorant binding to olfactory receptors, including the role of G-proteins and second messengers in generating an action potential.
Identify different types of olfactory disorders such as anosmia, hyposmia, hyperosmia, and dysosmia, including their potential causes.
Key Topics:
Olfactory Genes:
3% of the human genome accounts for olfactory genes.
400 genes for odorant receptors.
Olfactory Membrane:
Located in the superior part of the nasal cavity.
Medially: Folds downward along the superior septum.
Laterally: Folds over the superior turbinate and upper surface of the middle turbinate.
Total surface area: 5-10 square centimeters.
Olfactory Mucosa:
Olfactory Cells: Bipolar nerve cells derived from the CNS (100 million), with 4-25 olfactory cilia per cell.
Sustentacular Cells: Produce mucus and maintain ionic and molecular environment.
Basal Cells: Replace worn-out olfactory cells with an average lifespan of 1-2 months.
Bowman’s Gland: Secretes mucus.
Stimulation of Olfactory Cells:
Odorant dissolves in mucus and attaches to receptors on olfactory cilia.
Involves a cascade effect through G-proteins and second messengers, leading to depolarization and action potential generation in the olfactory nerve.
Quality of a Good Odorant:
Small (3-20 Carbon atoms), volatile, water-soluble, and lipid-soluble.
Facilitated by odorant-binding proteins in mucus.
Membrane Potential and Action Potential:
Resting membrane potential: -55mV.
Action potential frequency in the olfactory nerve increases with odorant strength.
Adaptation Towards the Sense of Smell:
Rapid adaptation within the first second, with further slow adaptation.
Psychological adaptation greater than receptor adaptation, involving feedback inhibition from the central nervous system.
Primary Sensations of Smell:
Camphoraceous, Musky, Floral, Pepperminty, Ethereal, Pungent, Putrid.
Odor Detection Threshold:
Examples: Hydrogen sulfide (0.0005 ppm), Methyl-mercaptan (0.002 ppm).
Some toxic substances are odorless at lethal concentrations.
Characteristics of Smell:
Odor blindness for single substances due to lack of appropriate receptor protein.
Behavioral and emotional influences of smell.
Transmission of Olfactory Signals:
From olfactory cells to glomeruli in the olfactory bulb, involving lateral inhibition.
Primitive, less old, and new olfactory systems with different path
MANAGEMENT OF ATRIOVENTRICULAR CONDUCTION BLOCK.pdfJim Jacob Roy
Cardiac conduction defects can occur due to various causes.
Atrioventricular conduction blocks ( AV blocks ) are classified into 3 types.
This document describes the acute management of AV block.
micro teaching on communication m.sc nursing.pdfAnurag Sharma
Microteaching is a unique model of practice teaching. It is a viable instrument for the. desired change in the teaching behavior or the behavior potential which, in specified types of real. classroom situations, tends to facilitate the achievement of specified types of objectives.
Title: Sense of Taste
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the structure and function of taste buds.
Describe the relationship between the taste threshold and taste index of common substances.
Explain the chemical basis and signal transduction of taste perception for each type of primary taste sensation.
Recognize different abnormalities of taste perception and their causes.
Key Topics:
Significance of Taste Sensation:
Differentiation between pleasant and harmful food
Influence on behavior
Selection of food based on metabolic needs
Receptors of Taste:
Taste buds on the tongue
Influence of sense of smell, texture of food, and pain stimulation (e.g., by pepper)
Primary and Secondary Taste Sensations:
Primary taste sensations: Sweet, Sour, Salty, Bitter, Umami
Chemical basis and signal transduction mechanisms for each taste
Taste Threshold and Index:
Taste threshold values for Sweet (sucrose), Salty (NaCl), Sour (HCl), and Bitter (Quinine)
Taste index relationship: Inversely proportional to taste threshold
Taste Blindness:
Inability to taste certain substances, particularly thiourea compounds
Example: Phenylthiocarbamide
Structure and Function of Taste Buds:
Composition: Epithelial cells, Sustentacular/Supporting cells, Taste cells, Basal cells
Features: Taste pores, Taste hairs/microvilli, and Taste nerve fibers
Location of Taste Buds:
Found in papillae of the tongue (Fungiform, Circumvallate, Foliate)
Also present on the palate, tonsillar pillars, epiglottis, and proximal esophagus
Mechanism of Taste Stimulation:
Interaction of taste substances with receptors on microvilli
Signal transduction pathways for Umami, Sweet, Bitter, Sour, and Salty tastes
Taste Sensitivity and Adaptation:
Decrease in sensitivity with age
Rapid adaptation of taste sensation
Role of Saliva in Taste:
Dissolution of tastants to reach receptors
Washing away the stimulus
Taste Preferences and Aversions:
Mechanisms behind taste preference and aversion
Influence of receptors and neural pathways
Impact of Sensory Nerve Damage:
Degeneration of taste buds if the sensory nerve fiber is cut
Abnormalities of Taste Detection:
Conditions: Ageusia, Hypogeusia, Dysgeusia (parageusia)
Causes: Nerve damage, neurological disorders, infections, poor oral hygiene, adverse drug effects, deficiencies, aging, tobacco use, altered neurotransmitter levels
Neurotransmitters and Taste Threshold:
Effects of serotonin (5-HT) and norepinephrine (NE) on taste sensitivity
Supertasters:
25% of the population with heightened sensitivity to taste, especially bitterness
Increased number of fungiform papillae
Explore natural remedies for syphilis treatment in Singapore. Discover alternative therapies, herbal remedies, and lifestyle changes that may complement conventional treatments. Learn about holistic approaches to managing syphilis symptoms and supporting overall health.
Flu Vaccine Alert in Bangalore Karnatakaaddon Scans
As flu season approaches, health officials in Bangalore, Karnataka, are urging residents to get their flu vaccinations. The seasonal flu, while common, can lead to severe health complications, particularly for vulnerable populations such as young children, the elderly, and those with underlying health conditions.
Dr. Vidisha Kumari, a leading epidemiologist in Bangalore, emphasizes the importance of getting vaccinated. "The flu vaccine is our best defense against the influenza virus. It not only protects individuals but also helps prevent the spread of the virus in our communities," he says.
This year, the flu season is expected to coincide with a potential increase in other respiratory illnesses. The Karnataka Health Department has launched an awareness campaign highlighting the significance of flu vaccinations. They have set up multiple vaccination centers across Bangalore, making it convenient for residents to receive their shots.
To encourage widespread vaccination, the government is also collaborating with local schools, workplaces, and community centers to facilitate vaccination drives. Special attention is being given to ensuring that the vaccine is accessible to all, including marginalized communities who may have limited access to healthcare.
Residents are reminded that the flu vaccine is safe and effective. Common side effects are mild and may include soreness at the injection site, mild fever, or muscle aches. These side effects are generally short-lived and far less severe than the flu itself.
Healthcare providers are also stressing the importance of continuing COVID-19 precautions. Wearing masks, practicing good hand hygiene, and maintaining social distancing are still crucial, especially in crowded places.
Protect yourself and your loved ones by getting vaccinated. Together, we can help keep Bangalore healthy and safe this flu season. For more information on vaccination centers and schedules, residents can visit the Karnataka Health Department’s official website or follow their social media pages.
Stay informed, stay safe, and get your flu shot today!
Couples presenting to the infertility clinic- Do they really have infertility...Sujoy Dasgupta
Dr Sujoy Dasgupta presented the study on "Couples presenting to the infertility clinic- Do they really have infertility? – The unexplored stories of non-consummation" in the 13th Congress of the Asia Pacific Initiative on Reproduction (ASPIRE 2024) at Manila on 24 May, 2024.
How to Give Better Lectures: Some Tips for Doctors
Enhancing Rare Disease Literature for Researchers and Patients
1. Enhancing accessibility of
rare disease literature for
researchers and patients
Erin D. Foster, MSLS
MLA Annual Conference
29 May 2017
2. Some backstory & co-authors
2
Mark Engelstad
OHSU
Nicole Vasilevsky
OHSU
Melissa Haendel
OHSU
Peter Robinson
The Jackson Laboratory
Sebastian Köhler
Charite
Chris Mungall
The Berkeley Lab
9. Human Phenotype Ontology (HPO)
<human-phenotype-ontology.github.io/>
Abnormality of vision
Abnormality of color vision
Abnormality of
binocular vision
Monochromacy
Dyschromatopsia
Achromatopsia
Red-green
dyschromatopsia
Dichromacy
9
11. How can patients be more
involved?
II
11Image credit to Aaron Kuehn
12. Adding layperson synonyms to the
Human Phenotype Ontology
12
Abnormality of vision
Abnormality of color vision
Abnormality of
binocular vision
Monochromacy
Dyschromatopsia
Achromatopsia
Red-green
dyschromatopsia
Dichromacy
13. Adding layperson synonyms to the
Human Phenotype Ontology
13
Abnormality of vision
Abnormality of color vision
Abnormality of
binocular vision
Monochromacy
Dyschromatopsia
Achromatopsia
Red-green
dyschromatopsia
Dichromacy
Synonym: Color
blindness
Synonym: Red-green
color blindness
14. Team laypersonese
14Image credit to Aaron Kuehn
Erin & Nicole
Mark
Systematically reviewed all of
HPO (i.e. 12,000 classes)
Searched for synonyms
• Medline Plus
• Mayo Clinic
• Wikipedia
Assigned synonyms or marked
existing as layperson
Quality Assurance
• Reviewed by 3 curators
• Checked for duplicated synonyms, valid
character-encoding, title case formatting, and
annotation consistency
• SNOMED CT
• Elements of
Morphology
18. Identifie
d
Screene
d
Include
d ‘case reports’[pubtype]
identified in PubMed
(n =1,778,204)
Records <=10 years
(n =532,130)
European Journal of Human
Genetics (EJHG)
(n =143)
Focused on journals
to narrow sample
size
18
Excluded PMIDs
listed in OMIM
(n=22,756)
Reported
EJHG sub-sample
(n =20)
Sub sample of
EJHG articles to
figure out workflow
19. Annotate disease, associated genes and
phenotypes for each paper
Gene: CHRNA7
Disease: 15q13.3 homozygous microdeletion syndrome
Phenotypes: severe cerebral visual impairment,
congenital hypotonia, refractory epilepsy
19
21. Challenges (in brief)
1. Maintaining consistency in HPO
term definitions and use
2. Establishing a curation
workflow
3. Ensuring annotation reliability
21
23. (some) Next steps
23
• Review of patient forums,
medical message boards
• Track and analyze user
comments
• Complete annotation of
literature sample
• Incorporate annotations
into databases (like
Monarch)
25. Acknowledgements
The OHSU Library
Melissa Haendel, PhD*
Nicole Vasilevsky, PhD*
Mark Engelstad, MD*
Sebastian Köhler, PhD*
Peter Robinson, PhD*
Chris Mungall, PhD*
Kathel Dunn, PhD
NLM Associate Fellowship Program
25
*involved in project work
discussed
