101 Matching Annotations
  1. Aug 2019
    1. autism spectrum disorder

      HP_0000729,DOID_2030,HP_0000739,ZP_0005531,SO_1000039

    2. ASDs are frequently associated with comorbid intellectual disability (ID), ranging between 30 and 60% of cases depending on the sampling methods and measurements used

      DOID_12849,HP_0000717

    3. ASDs are frequently associated with comorbid intellectual disability (ID), ranging between 30 and 60% of cases depending on the sampling methods and measurements used
      • obsolete Peripheral visual field constriction with 30-39 degrees central field preserved
      • mixed embryonal carcinoma and endodermal sinus neoplasm with seminoma of the testis
    1. Moreover, SCN2A appears to be one of the major genes in which mutations are detected in nonsyndromic intellectual disability (ID) or autism spectrum disorders (ASDs) by whole-exome sequencing6

      DOID_0060041,AUTISMC1000014,DOID_12849

    1. nnotate! Enable the sidebar via the button in the locati

      DOID_3981,DOID_7968

    2. using the sidebar on the ri

      HP_0031638,HP_0011605

    1. An annotation is considered to be a set of connected resources, typically including a body and target, and conveys that the body is related to the target.

      Structure of annotation

    1. The use of on-line, digital data has caused a revolution in the way scientific research is conducted. Inevery area of science, much investigation now depends not on new experiments, but on databases in whichexperimental evidence has been stored.

      Need for annotation for scientific research

    2. Most people will agree with the dictionary definition ofannotationas the process of adding comments ormaking notes on or upon something. Such notes have traditionally served a variety of purposes, includingexplaining, interpreting or describing some underlying text.

      Define annotation

    1. Figure 2: Link between terms (mentions) of a document and theontology entities

      Semantic annotation diagram

    2. The annotation process could be a source of differenttypes of problems, for example, (i) ambiguous annotations,when entities have been assigned to more than one concept inthe ontology, (ii) erroneous annotations, when the meaningof a text is not found in the ontology, and, (iii) falseannotations, when the annotation does not provide any valuefor the realization of a semantic search.

      Semantic annotations challenges

    3. The semantic annotation has been applied in differentareas of knowledge. For example, it has been applied inbiological systems for the identification of biomedical entitiessuch as genes, proteins, and their relationships; also, it hasbeen applied in news analysis for identification of people,organizations, and places.

      Semantic annotations applications in biological field

    4. The annotation playsan important role in a variety of semantic applications, suchas generation of linked data, extraction of open information,alignment of ontologies, and semantic search. Specifically,semantic search allows users to express their informationneeds in terms of the knowledge base concepts. Unliketraditional keyword-based search, semantic search can makeuse of semantic relationships in the ontology to accomplishnew tasks, such as refining user queries with broader or morespecific concepts

      Uses of semantic annotations. Benefits/advantages

    5. The semantic annotation of a document consists infinding mappings between text chunks of a document andthe instances or individuals in ontology.

      Semantic annotation definition

    6. Ontologies are a key component of semantic association,which is the process to formalizing knowledge through thelinking of words or phrases of plain text (mentions or namedentities) with elements of the ontology (concepts or entitie

      Ontology definition

    7. The rapid growth of the web has generated an enormousamount of information in the form of unstructured doc-uments. Search engines have become common and basictools for users. However, engines still have difficulties inperforming searches because search methods are based onkeywords, and they do not capture and do not explore themeaning and context of the need of the user. This challengehas drawn attention of several research groups which areinterested in solving the issues associated with informationstorage and search and retrieval of information in thisenormous cumulus of data

      Motivation for semantic annotation

    1. A typical process of semantic enrichment includes:

      Semantic enrichment process. May be this is how they do deep phenotyping??

    2. For instance, to semantically annotate chosen concepts in the sentence “Aristotle, the author of Politics, established the Lyceum” means to identify Aristotle as a person and Politics as a written work of political philosophy, and to further index, classify and interlink the identified concepts in a semantic graph database, also known as a, triplestore. In this case, Aristotle can be linked to his date of birth, his teachers, his works, etc. Politics can be linked to its subject, its date of creation, etc. Given the semantic metadata about the above sentence and its links to other (external or internal) formal knowledge, algorithms will be able to automatically:

      impact of semantic annotation in associate the meaning of the associated content

    3. When a document (or another piece of content, e.g., video) is semantically tagged, it becomes a source of information that is easy to interpret, combine and reuse by our computers.

      Semantic annotation making web documents readable by machine

    4. Semantic annotation (also known as semantic tagging or semantic enrichment) is the process of attaching additional information to various concepts (e.g., people, things, places, organizations, etc.) in a given text or any other content. Unlike classic text annotations, which are for the reader’s reference, semantic annotations are used by machines.

      Define semantic annotation

    1. The aim of the Semantic Web is to make the information on the Web understandable and useful to computer applications and in addition to humans. “The Semantic Web is an extension of the current web in which information is given well-defined meaning, better enabling computers and people to work in cooperation"(Berners-Lee, Hendler et al. 2001). The Semantic Web is a vision for the future of the Web, in which information is given explicit meaning, making it easier for machines to automatically process and integrate the information available on the Web.

      Define semantic web

    2. This limitation arises because most documents on the Web are written in HTML (HTML 2007), a language that is useful for visual presentation but which is semantically limited. As a result, humans can read and understand HTML Web

      Limitation of HTML web

    3. The aim of this chapter is to present the Web Ontology Language (OWL) which can be used to develop Semantic Web applications that understand information and data on the Web.

      USE OF OWL

    1. comprehensive bioinformatic resource for analysis of human diseases and phenotypes and serves as a computational bridge between genome biology and clinical medicine” (Köhler et al., 2017)

      DEFINE hpo

    1. An ontology is a data model that represents concepts, attributes, and relationships in the form of a directed acyclic graph

      DEFINE ONTOLOGY

    2. Each term in the HPO describes a phenotypic abnormality, such as Atrial septum defect. Terms are related to parent terms by “is a” relationships. The structure of the HPO, which allows a term to have multiple parent terms, enables different aspects of phenotypic abnormalities to be explored (see Figure 1 for an example). The HPO itself does not describe individual disease entities but, rather, the phenotypic abnormalities associated with them. The majority of the HPO terms describe organ abnormalities, but separate ontologies are provided for describing the mode of inheritance and the onset and clinical course. We have used the HPO terms to annotate all entries of OMIM with a clinical-synopsis section. Clinical entities are annotated to the most specific terms possible. The true-path rule17 applies to the terms of the HPO. That is, if a disease is annotated to the term Atrial septal defect, then all of the ancestors of this term, such as Abnormality of the cardiac septa, also apply. The structure of the HPO, therefore, allows flexible searches for disease entities according to phenotypic abnormalities, with a broad or narrow focus.

      STRUCTURE OF HPO

    1. Consider, for example, the application of ontologies in the field of health care. Medical professionals use them to represent knowledge about symptoms, diseases, and treatments. Pharmaceutical companies use them to represent information about drugs, dosages, and allergies. Combining this knowledge from the medical and pharmaceutical communities with patient data enables a whole range of intelligent applications such as decision support tools that search for possible treatments; systems that monitor drug efficacy and possible side effects; and tools that support epidemiological research.

      Application of ontology in health

    2. A general example may help. A bookseller may want to integrate data coming from different publishers. The data can be imported into a common RDF model, eg, by using converters to the publishers’ databases. However, one database may use the term “author”, whereas the other may use the term “creator”. To make the integration complete, and extra definition should be added to the RDF data, describing the fact that the relationship described as “author” is the same as “creator”. This extra piece of information is, in fact, a vocabulary (or an ontology), albeit an extremely simple one

      Ontology example

    3. On the Semantic Web, vocabularies define the concepts and relationships (also referred to as “terms”) used to describe and represent an area of concern. Vocabularies are used to classify the terms that can be used in a particular application, characterize possible relationships, and define possible constraints on using those terms. In practice, vocabularies can be very complex (with several thousands of terms) or very simple (describing one or two concepts only).

      Ontology definition

    1. nd running. It's time to start annotati
      • obsolete Acral ulceration and osteomyelitis leading to autoamputation of the digits (feet)
      • Combined hamartoma of the retinal pigment epithelium and retina
      • sex-limited autosomal dominant inheritance
      • sex-limited autosomal recessive inheritance
      • Postoperative
      • OperationHistory
      • MedicationHistory
    1. The term was coined by Tim Berners-Lee for a web of data (or data web)[3] that can be processed by machines[4]—that is, one in which much of the meaning is machine-readable.

      what semantic web mean in relation to machines

    2. The Semantic Web is an extension of the World Wide Web through standards by the World Wide Web Consortium (W3C).[1] The standards promote common data formats and exchange protocols on the Web, most fundamentally the Resource Description Framework (RDF). According to the W3C, "The Semantic Web provides a common framework that allows data to be shared and reused across application, enterprise, and community boundaries".[2] The Semantic Web is therefore regarded as an integrator across different content, information applications and systems.

      definition of semantic web

    1. The Semantic Web is an extension of the current web in which information is given well-defined meaning, better enabling computers and people to work in cooperation.

      definitnion of semantic web

    1. to provide sufficient flexibility to be able to represent all databases, and logic rules to link them together to great added value. The first steps in this direction were taken by the World-Wide Web Consortium (W3C) in defining Resource Description Framework (RDF)

      originating of RDF

    2. The Semantic Web concept is to do for data what HTML did for textual information systems

      semantic web vs html

    3. At the outset of the Web, the field of hypertext was one which had shown much initial promise but little wide scale deployment. Its conversion to a global scalable system was to change that. In the meantime, much work in knowledge representation (KR) -- in ontology, interchange languages, and agent infrastructure -- has demonstrated the viability of KR as a basis for agent interaction while simultaneously highlighting the importance of support for heterogeneity and decentralization. At present, the field of knowledge representation has shown much initial promise but little truly widespread deploymen

      knowledge representation and ontology

    4. When the World Wide Web was proposed a decade ago it was envisioned not only as a medium for human communication but also one of machine communication. The second half of that hope is as yet unrealized, with the frustrating result that vast amounts of data available to the human enquirer cannot practically be analysed and combined by machine.

      Machines for world wide web

  2. Jul 2019
    1. Annotation Types There are a few types of annotations that can be created with the application
      • Atypical small acinar proliferation of the prostate gland
      • diabetes mellitus insulin dependent type, uncontrolled, with ophthalmic manifestations
      • Predictable_abnormal_idiosyncratic_negative_response_to_one_or_more_sensory_stimuli_with_substantial_interference_with_family_routines
    1. Authentication in SPA (ReactJS and VueJS) the right wayCookie, session, token, JWT, attacks, where to store token, security concerns? Everything you need to know is here.
      • hypertension secondary to renal disease, complicating pregnancy, childbirth and the puerperium
      • Spontaneous_imitation_limited_to_a_few_familiar_routines_that_are_not_incorporated_into_play
      • Impaired growth-hormone response to glucagon stimulation test
    1. e! Enable the sidebar via the button in the location bar.
      • Ulnar deviation of the 4th finger
      • Ulnar deviation of the hand or of fingers of the hand
      • Ulnar deviation of the 5th finger
      • MedicationforEuthanasia
      • AntineoplaticDrugAgentTherapy
    2. Try it on this sentence.
      • Double outlet right ventricle with non-committed ventricular septal defect and pulmonary stenosis
      • Double outlet right ventricle with subpulmonary ventricular septal defect without pulmonary stenosis
    3. some notes

    1. otate! Enable the sidebar via the button in the location bar.
      • congenital diarrhea 5 with tufting enteropathy
      • transitional cell carcinoma of the ureter with mixed differentiation
      • genotype-phenotype association
      • simple_sequence_length_variation
      • organellar plasmy
      • LanguageTherapy
    1. and annotate! Enable the sidebar via the button in the location bar
      • Partial duplication of the middle phalanges of the hand
      • Partial duplication of the middle phalanx of the 2nd toe
      • Partial duplication of the middle phalanx of the 4th finger
      • Partial duplication of the middle phalanx of the 2nd finger
      • heteroplasmic mitochondrial inheritance
      • sequence_length_variation
      • sex-limited autosomal dominant inheritance
    1. otate! Enable the sidebar via the button in the location bar.
      • Ulnar deviation of the 4th finger
      • Ulnar deviation of the 5th finger
      • Supraventricular tachycardia with a concealed accessory pathway on the right free wall
    1. annotate! Enable the sidebar via the button in the location bar.
      • Triangular shaped proximal phalanx of the 4th finger
      • separation anxiety disorder
    1. tate! Enable the sidebar via the button in the location bar.
      • Ulnar deviation of the 4th finger
      • Ulnar deviation of the 5th finger
    1. Go forth and annotate! Enable the sidebar via the button in the location bar
      • Partial duplication of the middle phalanx of the 4th finger
      • Partial duplication of the middle phalanx of the 5th finger
      • Rare_or_No_Social_Approaches_of_Showing_and_Directing_Attention
    1. idebar via the button in the location bar.
      • Ulnar deviation of the 4th finger
      • Ulnar deviation of the 5th finger
      • sequence_length_variation
      • heteroplasmic mitochondrial inheritance
      • Definite_unusual_and_marked_resistance_to_trivial_changes_in_the_environment
      • Spontaneous_imitation_limited_to_a_few_familiar_routines_that_are_not_incorporated_into_play
      • One_or_More_Relationships_That_Involve_Some_Personal_Shared_Activities
    1. at can be created with the applicatio
      • Dense calcifications in the cerebellar dentate nucleus
      • Disorganization of the anterior cerebellar vermis
      • MedicationforNutrition
      • OccupationalTherapy
      • Speech_tendsOrTended_to_be_more_repetitive_than_most_subject
      • One_or_more_activities_that_subject_has_to_preform_in_a_special_way_if_disrupted_appears_to_be_under_MARKED_pressure
    1. with Everthing ElseHave all your important software under one platform; HR, Inventory, Budget Accounts and
      • Contracture of the metacarpophalangeal joint of the 2nd finger
      • EMG: decremental response of compound muscle action potential to repetitive nerve stimulation
      • EMG: incremental response of compound muscle action potential to repetitive nerve stimulation
      • Contracture of the distal interphalangeal joint of the 2nd finger
      • Anxiety
      • Atrial fibrillation
    1. tions are either public and visible to everyone or
      • Subsarcolemmal accumulations of abnormally shaped mitochondria
      • obsolete Ectopic anterior pituitary
      • Glial remnants anterior to the optic disc
      • Refractory sideroblastic anemia
    2. types of annotations that can be created
      • Premature delivery because of cervical insufficiency or membrane fragility
      • Atresia of the Eustachian tube
    1. e are a few types of annotations that can be created with the ap
      • Progressive loss of facial adipose tissue
      • Dissociated sensory loss
      • Early ossification of capital femoral epiphyses
      • Gonadal dysgenesis with female appearance, male
    1. Create a note by selecting some text and clicking the button
      • Ameliorated by immunosuppresion
      • Neoplasm by anatomical site
      • Ameliorated by heat
    1. nnotations that can be created
      • Premature delivery because of cervical insufficiency or membrane fragility
    2. Create an account using the sidebar on the right of the screen.
      • Common origin of the right brachiocephalic artery and left common carotid artery
    1. You can reply to any annotation by using the reply action on every card. Privacy
      • Double outlet right ventricle with non-committed ventricular septal defect and pulmonary stenosis
    2. There are a few types of annotations that can be created with the application: Notes Create a note by selecting some text and clicking the button
      • obsolete Transposition of the great arteries with ventricular septal defect
      • Exacerbated by methylxanthine ingestion
      • Very severe constriction of peripheral visual field
      • Cervical vertebral bodies with decreased anteroposterior diameter
    1. Now you have the extension up and running. It's time to start annotating some documents. Create an account using the sidebar on the right of the screen.
      • Double outlet right ventricle with non-committed ventricular septal defect and pulmonary stenosis
      • Anomalous origin of the left common carotid artery from the brachiocephalic artery
    1. Annotation Types There are a few types of annotations that can be created with the application: Notes Create a note by selecting some text and clicking the button Highlights Highlights can be created by clicking the button. Try it on this sentence. Replies You can reply to any annotation by using the reply action on every card.
      • Exacerbated by methylxanthine ingestion
      • Triggered by ethanol ingestion
      • Ameliorated by ethanol ingestion
    2. These annotations are visible to everyone both in the document itself and our public stream. Private Private annotations are visible only to you when logged in. Show/Hide Highlights Use the button to toggle highlight visibility on a page.
      • Non-caseating epithelioid cell granulomatosis
      • Yellow-brown discoloration of the teeth
      • Hemiareflexia
      • Hemianopia
      • Hemihypsarrhythmia
    1. Notes Create a note by selecting some text and clicking the button Highlights Highlights can be created by clicking the button. Try it on this sentence. Replies You can reply to any annotation by using the reply action on every card.
      • Anomalous origin of the left common carotid artery from the main pulmonary artery
      • Ameliorated by carbohydrate ingestion
      • Double outlet right ventricle with non-committed ventricular septal defect without pulmonary stenosis
    1. Now you have the extension up and running. It's time to start annotating some documents. Create an account using the sidebar on the right of the screen. Go forth and annotate! Enable the sidebar via the button in the location bar.
      • Anomalous origin of the left anterior descending artery from the pulmonary artery
      • Anomalous origin of the right subclavian artery from the descending aorta
      • Supraventricular tachycardia with an accessory connection mediated pathway
    1. There are a few types of annotations that can be created with the application: Notes Create a note by selecting some text and clicking the button Highlights Highlights can be created by clicking the button. Try it on this sentence. Replies
      • Exacerbated by methylxanthine ingestion
      • Triggered by ethanol ingestion
    1. View the product roadmap to check out what we're working on. Request features, report bugs and meet other users in our discussion forums. If you need help please don't hesitate to get in touch. Visit our website to learn more about the project.
      • Decreased specific antibody response to protein-conjugated polysaccharide vaccine
      • obsolete Acral ulceration and osteomyelitis leading to autoamputation of the digits (feet)
      • Anomalous insertion of papillary muscle directly into anterior mitral leaflet
    1. Annotation Types There are a few types of annotations that can be created with the application: Notes Create a note by selecting some text and clicking the button
      • obsolete Atrioventricular canal defect with right ventricle aorta and pulmonary atresia
      • Congenitally corrected transposition of the great arteries with ventricular septal defect
    1. Now you have the extension up and running. It's time to start annotating some documents. Create an account using the sidebar on the right of the screen. Go forth and annotate! Enable the sidebar via the button in the location bar. Annotation Types There are a few types of annotations that can be created with the application: Notes
      • Supraventricular tachycardia with a manifest accessory pathway on the right free wall
      • Supraventricular tachycardia with a manifest accessory pathway on the left free wall
      • Anomalous origin of the left anterior descending artery from the pulmonary artery
      • Contractures of the metatarsophalangeal joint of the hallux
      • Double outlet right ventricle with subaortic ventricular septal defect and pulmonary stenosis
    1. uccessful PeopleInstead of looking for traits to emulate, focus on ones to avoid
      • Green teeth
      • Bilateral vertebral artery hypoplasia
    1. Notes Create a note by selecting some text and clicking the button Highlights Highlights can be created by clicking the button. Try it on this se
      • Increased circulating surfactant protein level
      • Decreased retinol-binding protein level
    2. Create an account using the sidebar on the right of the screen. Go forth and annotate! Enable the sidebar via the button in the location bar.
      • Anomalous origin of the right subclavian artery from the descending aorta
      • Increased urinary high-mannose-type oligosaccharide
      • Sacralization of the fifth lumbar vertebra
    1. ou have the extension up and running. It's time to start annotating some documents. Create an account using the sidebar on the right of the screen. Go forth and annotate! Enable the sidebar via the button in the location bar.
      • Anxiety
      • Atrial fibrillation
      • Agoraphobia
    1. Highlights Highlights can be created by clicking the button. Try it on this sentence. Replies You can reply to any annotation by using the reply action on every card.
      • Patchy osteosclerosis
    2. ighlights Highlights can be created by
      • Exercise-induced hemolysis
      • Cold-induced hemolysis
      • Recurrent abscess formation
      • Agoraphobia
      • Anxiety
      • Abnormal fear/anxiety-related behavior
    3. Enable the sidebar via the button in the location bar.
      • Superiorly positioned umbilicus
      • Abnormal location of the eyebrow
      • Abnormal anatomic location of the heart
      • Prominent umbilicus
    1. Go forth and annotate! Enable the sidebar via the button in the location bar.
      • Abnormal umbilicus morphology
      • Abnormal location of the eyebrow
      • Abnormal anatomic location of the heart
      • Dot-and-blot retinal hemorrhage
    2. There are a few types of annotations that can be created with the application:
      • Past obstetric history
      • Past medical history
    1. Go forth and annotate! Enable the sidebar via the button in the location bar.
      • Superiorly positioned umbilicus
      • Abnormal umbilicus morphology
      • Abnormal location of the eyebrow
    1. Go forth and annotate! Enable the sidebar via the button in the location bar.
      • Abnormal location of the eyebrow
      • Atrophy/Degeneration involving the spinal cord
      • Prominent umbilicus
    1. Now you have the extension up and running. It's time to start annotating some documents. Create an account using the sidebar on the right of the screen. Go forth and annotate! Enable the sidebar via the button in the location bar. Annotation Types There are a few types of annotations that can be created with the application: Notes Create a note by selecting some text and clicking the button Highlights Highlights can be created by clicking the button. Try it on this sentence. Replies You can reply to any annotation by using the reply action on every card.
      • Reduced forced expiratory volume in one second
      • Alternating esotropia
      • Abnormal hepatic echogenicity
      • Bacterial cell casts
      • Superiorly positioned umbilicus
      • Patchy sclerosis of the middle phalanx of the 5th toe
      • Impaired two-point discrimination
      • Patchy sclerosis of the proximal phalanx of the 5th toe
      • Reduced granulocyte CD18 level
      • Patchy sclerosis of the proximal phalanx of the 4th toe
      • Patchy sclerosis of the middle phalanx of the 4th toe
    1. Create an account using the sidebar on the right of the screen. Go forth and annotate! Enable the sidebar via the button in the location bar
      • Abnormal right ventricle morphology
      • Increased circulating galectin-3 level
      • Telangiectases of the cheeks
    1. Go forth and annotate! Enable the sidebar via the button in the location bar.
      • Enlarged cisterna magna
      • Pancreas divisum
      • Dot-and-blot retinal hemorrhage
    1. t can be created with the application: Notes Create a note by selecting some text and clicking the button Highlights Highlights can be created by clicking the button. Try it on this sentence. Replies You can reply to any annotation by using the reply action on every card.
      • Reduced granulocyte CD18 level
      • Impaired two-point discrimination
    2. o forth and annotate! Enable the sidebar via the button in the location bar.
      • Prolonged bleeding after dental extraction
      • Anorexia
      • Past medical history
      • Past obstetric history
      • Fulminant hepatitis
      • Recurrent abscess formation
  3. Jun 2019
    1. Go forth and annotate! Enable the sidebar via the button in the location bar.
      • term 3
    1. t a sharable link to th
      • term 4
    2. ecting some text and clicking
      • term 1
    3. o forth and annotate! Enable the sidebar via the button in the location bar.
      • term 1
      • term 3
    1. sidebar via the button in the location bar.
      • term 4
      • term 5
      • term 6
    1. Go forth and annotate! Enable the sidebar via the button in the location bar.
      • term 2
      • term 3
    1. Use the button to toggle highlight visibility on a page.
      • term 2
      • term 3
    1. ate! Enable the sidebar via the button in the location bar.
      • term 2
    1. o forth and annotate! Enable the sidebar via the button in the location bar.
      • term 2
    1. and annotate! Enable the sidebar via the button in the location bar.
      • term 2
      • term 3
    1. your career in tech. It is a different kind of graduate programme focused on leadership, designed to create the next-g

      ddddd

    1. USINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUC

      a test annotation

  4. Apr 2019
    1. Most ontologies are structured as directed acyclic graphs (DAG), which are similar to hierarchies but differ in that a more specialized term (child) can be related to more than one less specialized term (parent).

      HPO Structure

  5. Mar 2019
    1. DevOps is a term for a group of concepts that

      what is devops