The Proteomics Standards Initiative ( PSI ) is a working group of the Human Proteome Organization . It aims to define data standards for proteomics to facilitate data comparison , exchange and verification .
42-435: The Proteomics Standards Initiative focuses on the following subjects: minimum information about a proteomics experiment defines the metadata that should be provided along with a proteomics experiment. a data markup language for encoding the data, and metadata ontologies for consistent annotation and representation. Minimum information about a proteomics experiment ( MIAPE ) is a minimum information standard , created by
84-495: A diagnosis of exclusion . Even if it does not result in a single probable disease or condition, it can at least rule out any imminently life-threatening conditions. Unless the provider is certain of the condition present, further medical tests, such as medical imaging, are performed or scheduled in part to confirm or disprove the diagnosis but also to document the patient's status and keep the patient's medical history up to date. If unexpected findings are made during this process,
126-480: A process of elimination or at least of rendering the entries more or less probable by further medical tests and other processing, aiming to reach the point where only one candidate disease or condition remains as probable. The result may also remain a list of possible conditions, ranked in order of probability or severity. Such a list is often generated by computer-aided diagnosis systems. The resultant diagnostic opinion by this method can be regarded more or less as
168-402: A brief summation or an extensive formulation, even taking the form of a story or metaphor. It might be a means of communication such as a computer code through which it triggers payment, prescription, notification, information or advice. It might be pathogenic or salutogenic . It is generally uncertain and provisional. Once a diagnostic opinion has been reached, the provider is able to propose
210-817: A controlled vocabulary to use with the previous file formats. The molecular interactions working group of PSI only works on PSI MI XML , a data exchange format, and on its corresponding ontologies. They have published the MIMIx guidelines (minimum information about a molecular interaction experiment) Study design and sample generation and statistical analysis of data MIAPE recommendations are also being planned or drafted. Several standard-compliant proteomics repositories exist, allowing researchers to publish their data while enforcing MIAPE guidelines. For example: MIAPEGelDB (for gel electrophoresis data), PRIDE (for mass spectrometry data), and ProteoRed MIAPE Generator tool (for gel electrophoresis and mass spectrometry data) It
252-760: A controlled vocabulary to use with the previous file formats. The molecular interactions working group of PSI only works on PSI MI XML , a data exchange format, and on its corresponding ontologies. They have published the MIMIx guidelines (minimum information about a molecular interaction experiment) Study design and sample generation and statistical analysis of data MIAPE recommendations are also being planned or drafted. Several standard-compliant proteomics repositories exist, allowing researchers to publish their data while enforcing MIAPE guidelines. For example: MIAPEGelDB (for gel electrophoresis data), PRIDE (for mass spectrometry data), and ProteoRed MIAPE Generator tool (for gel electrophoresis and mass spectrometry data) It
294-523: A different therapy so it may be limited to cases where no diagnosis can be made. The term diagnostic criteria designates the specific combination of signs and symptoms , and test results that the clinician uses to attempt to determine the correct diagnosis. Some examples of diagnostic criteria, also known as clinical case definitions , are: Clinical decision support systems are interactive computer programs designed to assist health professionals with decision-making tasks. The clinician interacts with
336-490: A disease is diagnosed correctly, but the diagnosis is irrelevant. A correct diagnosis may be irrelevant because treatment for the disease is not available, not needed, or not wanted. Most people will experience at least one diagnostic error in their lifetime, according to a 2015 report by the National Academies of Sciences, Engineering, and Medicine . Causes and factors of error in diagnosis are: When making
378-457: A management plan, which will include treatment as well as plans for follow-up. From this point on, in addition to treating the patient's condition, the provider can educate the patient about the etiology , progression, prognosis , other outcomes, and possible treatments of her or his ailments, as well as providing advice for maintaining health. A treatment plan is proposed which may include therapy and follow-up consultations and tests to monitor
420-542: A mass spectrometer, which is a merge of the previous mzData (developed by PSI) and mzXML (developed at the Seattle Proteome Center at the Institute for Systems Biology); mzIdentML, for Mass spectra informatics analysis that capture the results of the identification of proteins and peptides from mass spectrometry data; and TraML, for selected reaction monitoring input file. Finally, they develop MS CV ,
462-619: A medical diagnosis, a lag time is a delay in time until a step towards diagnosis of a disease or condition is made. Types of lag times are mainly: Long lag times are often called "diagnostic odyssey". The first recorded examples of medical diagnosis are found in the writings of Imhotep (2630–2611 BC) in ancient Egypt (the Edwin Smith Papyrus ). A Babylonian medical textbook, the Diagnostic Handbook written by Esagil-kin-apli ( fl. 1069–1046 BC), introduced
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#1732787294046504-414: A number of methods or techniques that can be used in a diagnostic procedure, including performing a differential diagnosis or following medical algorithms . In reality, a diagnostic procedure may involve components of multiple methods. The method of differential diagnosis is based on finding as many candidate diseases or conditions as possible that can possibly cause the signs or symptoms, followed by
546-507: A proteomics experiment The Proteomics Standards Initiative ( PSI ) is a working group of the Human Proteome Organization . It aims to define data standards for proteomics to facilitate data comparison , exchange and verification . The Proteomics Standards Initiative focuses on the following subjects: minimum information about a proteomics experiment defines the metadata that should be provided along with
588-513: A proteomics experiment. a data markup language for encoding the data, and metadata ontologies for consistent annotation and representation. Minimum information about a proteomics experiment ( MIAPE ) is a minimum information standard , created by the Proteomics Standards Initiative of the Human Proteome Organization , for reporting proteomics experiments. You can't just introduce the results of an analysis, it
630-458: A recommendation and has been published. The corresponding data exchange format is called GelML, and a stable version was released in late 2007. The gel electrophoresis working group also focuses on image analysis with the gel image informatics recommendation that is currently in the public review phase while the corresponding exchange format is only a draft (as of April 2009). The sample processing working group defines requirements concerning all
672-420: A result of an incidental finding of a sign unrelated to the parameter of interest, such as can occur in comprehensive tests such as radiological studies like magnetic resonance imaging or blood test panels that also include blood tests that are not relevant for the ongoing diagnosis. General components which are present in a diagnostic procedure in most of the various available methods include: There are
714-599: Is expected that journal editors will eventually request authors to publish all their data to such repositories before publication . There are similar initiatives that try to define minimal requirements. For microarrays the MGED Society defined the minimum information about a microarray experiment (MIAME). The standards for reporting of diagnostic accuracy (STARD) is available for studies reporting medical diagnosis accuracies . Medical diagnosis Medical diagnosis (abbreviated Dx , D x , or D s )
756-480: Is expected that journal editors will eventually request authors to publish all their data to such repositories before publication. There are similar initiatives that try to define minimal requirements. For microarrays the MGED Society defined the minimum information about a microarray experiment (MIAME). The standards for reporting of diagnostic accuracy (STARD) is available for studies reporting medical diagnosis accuracies . Minimum information about
798-527: Is intended to specify all the information necessary to interpret the experiment results unambiguously and to potentially reproduce the experiment. While the MIAPE guidelines define the content required for compliant reports, it does not specify the format in which this data should be presented (which is left to the corresponding *ML format, also defined by PSI ), nor does it define how to perform experiments. Several working groups work on several documents covering
840-459: Is not the same as the individual's diagnosis.) A total evaluation of a condition is often termed a diagnostic workup. A diagnostic procedure may be performed by various healthcare professionals such as a physician , physiotherapist , dentist , podiatrist , optometrist , nurse practitioner , healthcare scientist or physician assistant . This article uses diagnostician as any of these person categories. A diagnostic procedure (as well as
882-425: Is the process of determining which disease or condition explains a person's symptoms and signs . It is most often referred to as a diagnosis with the medical context being implicit. The information required for a diagnosis is typically collected from a history and physical examination of the person seeking medical care. Often, one or more diagnostic procedures , such as medical tests , are also done during
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#1732787294046924-564: The Greek word διάγνωσις ( diágnōsis ) from διαγιγνώσκειν ( diagignṓskein ), meaning "to discern, distinguish". Diagnosis can take many forms. It might be a matter of naming the disease, lesion, dysfunction or disability. It might be a management-naming or prognosis-naming exercise. It may indicate either degree of abnormality on a continuum or kind of abnormality in a classification. It is influenced by non-medical factors such as power, ethics and financial incentives for patient or doctor. It can be
966-409: The correlation of various pieces of information followed by the recognition and differentiation of patterns. Occasionally the process is made easy by a sign or symptom (or a group of several) that is pathognomonic . Diagnosis is a major component of the procedure of a doctor's visit . From the point of view of statistics , the diagnostic procedure involves classification tests . A diagnosis, in
1008-525: The sample pre-processing steps that are carried out before gel electrophoresis or mass spectrometry is applied. Two documents concerning column chromatography and capillary electrophoresis are in the early draft stages and the Sample preparation and handling is still a project (as of April 2009). The data exchange format (spML) is also under development. Mass spectrometry and mass spectrometry informatics documents have been published as recommendations by
1050-413: The Proteomics Standards Initiative of the Human Proteome Organization , for reporting proteomics experiments. You can't just introduce the results of an analysis, it is intended to specify all the information necessary to interpret the experiment results unambiguously and to potentially reproduce the experiment. While the MIAPE guidelines define the content required for compliant reports, it does not specify
1092-445: The actual process of making a diagnosis is a cognitive process. A clinician uses several sources of data and puts the pieces of the puzzle together to make a diagnostic impression. The initial diagnostic impression can be a broad term describing a category of diseases instead of a specific disease or condition. After the initial diagnostic impression, the clinician obtains follow up tests and procedures to get more data to support or reject
1134-428: The condition and the progress of the treatment, if needed, usually according to the medical guidelines provided by the medical field on the treatment of the particular illness. Relevant information should be added to the medical record of the patient. A failure to respond to treatments that would normally work may indicate a need for review of the diagnosis. Nancy McWilliams identifies five reasons that determine
1176-568: The decision. Other methods that can be used in performing a diagnostic procedure include: Diagnosis problems are the dominant cause of medical malpractice payments, accounting for 35% of total payments in a study of 25 years of data and 350,000 claims. Overdiagnosis is the diagnosis of "disease" that will never cause symptoms or death during a patient's lifetime. It is a problem because it turns people into patients unnecessarily and because it can lead to economic waste ( overutilization ) and treatments that may cause harm. Overdiagnosis occurs when
1218-404: The different areas of proteomics : The gel electrophoresis working group defined reporting requirements for gel electrophoresis experiments. The document is at the stage of a recommendation and has been published. The corresponding data exchange format is called GelML, and a stable version was released in late 2007. The gel electrophoresis working group also focuses on image analysis with
1260-418: The early draft stages and the Sample preparation and handling is still a project (as of April 2009). The data exchange format (spML) is also under development. Mass spectrometry and mass spectrometry informatics documents have been published as recommendations by the mass spectrometry working group. The working group has released several data exchange format: the mzML, for the capture of data generated by
1302-405: The format in which this data should be presented (which is left to the corresponding *ML format, also defined by PSI), nor does it define how to perform experiments. Several working groups work on several documents covering the different areas of proteomics : The gel electrophoresis working group defined reporting requirements for gel electrophoresis experiments. The document is at the stage of
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1344-441: The gel image informatics recommendation that is currently in the public review phase while the corresponding exchange format is only a draft (as of April 2009). The sample processing working group defines requirements concerning all the sample pre-processing steps that are carried out before gel electrophoresis or mass spectrometry is applied. Two documents concerning column chromatography and capillary electrophoresis are in
1386-428: The initial hypothesis may be ruled out and the provider must then consider other hypotheses. In a pattern recognition method the provider uses experience to recognize a pattern of clinical characteristics. It is mainly based on certain symptoms or signs being associated with certain diseases or conditions, not necessarily involving the more cognitive processing involved in a differential diagnosis. This may be
1428-556: The mass spectrometry working group. The working group has released several data exchange format: the mzML, for the capture of data generated by a mass spectrometer, which is a merge of the previous mzData (developed by PSI) and mzXML (developed at the Seattle Proteome Center at the Institute for Systems Biology); mzIdentML, for Mass spectra informatics analysis that capture the results of the identification of proteins and peptides from mass spectrometry data; and TraML, for selected reaction monitoring input file. Finally, they develop MS CV ,
1470-652: The opinion reached thereby) does not necessarily involve elucidation of the etiology of the diseases or conditions of interest, that is, what caused the disease or condition. Such elucidation can be useful to optimize treatment, further specify the prognosis or prevent recurrence of the disease or condition in the future. The initial task is to detect a medical indication to perform a diagnostic procedure. Indications include: Even during an already ongoing diagnostic procedure, there can be an indication to perform another, separate, diagnostic procedure for another, potentially concomitant, disease or condition. This may occur as
1512-418: The original diagnosis and will attempt to narrow it down to a more specific level. Diagnostic procedures are the specific tools that the clinicians use to narrow the diagnostic possibilities. The plural of diagnosis is diagnoses . The verb is to diagnose, and a person who diagnoses is called a diagnostician . The word diagnosis / d aɪ . ə ɡ ˈ n oʊ s ɪ s / is derived through Latin from
1554-478: The output of a heart monitor. Such automated processes are usually deemed a "device" by the FDA and require regulatory approval. In contrast, clinical decision support systems that "support" but do not replace the clinician are deemed to be "Augmented Intelligence" if it meets the FDA criteria that (1) it reveals the underlying data, (2) reveals the underlying logic, and (3) leaves the clinician in charge to shape and make
1596-416: The primary method used in cases where diseases are "obvious", or the provider's experience may enable him or her to recognize the condition quickly. Theoretically, a certain pattern of signs or symptoms can be directly associated with a certain therapy, even without a definite decision regarding what is the actual disease, but such a compromise carries a substantial risk of missing a diagnosis which actually has
1638-462: The process. Sometimes the posthumous diagnosis is considered a kind of medical diagnosis. Diagnosis is often challenging because many signs and symptoms are nonspecific . For example, redness of the skin ( erythema ), by itself, is a sign of many disorders and thus does not tell the healthcare professional what is wrong. Thus differential diagnosis , in which several possible explanations are compared and contrasted, must be performed. This involves
1680-405: The sense of diagnostic procedure, can be regarded as an attempt at classification of an individual's condition into separate and distinct categories that allow medical decisions about treatment and prognosis to be made. Subsequently, a diagnostic opinion is often described in terms of a disease or other condition. (In the case of a wrong diagnosis, however, the individual's actual disease or condition
1722-402: The software utilizing both the clinician's knowledge and the software to make a better analysis of the patients data than either human or software could make on their own. Typically the system makes suggestions for the clinician to look through and the clinician picks useful information and removes erroneous suggestions. Some programs attempt to do this by replacing the clinician, such as reading
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1764-483: The use of empiricism , logic and rationality in the diagnosis of an illness or disease . Traditional Chinese Medicine , as described in the Yellow Emperor's Inner Canon or Huangdi Neijing , specified four diagnostic methods: inspection, auscultation-olfaction, inquiry and palpation . Hippocrates was known to make diagnoses by tasting his patients' urine and smelling their sweat. Medical diagnosis or
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