]> 0.9.0 2010-02-11 Alan Ruttenberg Burke Squires Influenza ontology Joanne Luciano Lindsay Cowell Lynn Schriml Melanie Courtot Meredith Keybl Richard Scheuermann Ryan Brinkman The influenza ontology is an application ontology that covers the natural, experimental and clinical realms related to influenza virus life cycle, infection and disease. It is an extension of the infectious disease ontology (IDO). Timothy Lebo amplified virus preparation RBS:rbs MC, 20101203: redefined as defined class after adding virus amplification process An amplified virus preparation is an organimal group representing a large number of copies of one or more viruses. enriched cell fraction RBS:rbs An enriched cell fraction is a cell fraction that has an increased concentration of one or more cell fraction components. MC, 20101203: added enrichment process and cell fraction from GO and restrictions to make this a defined class complementary ribonucleic acid role RBS:rbs A complementary ribonucleic acid is a biological macromolecule role played by a RNA molecule that serves as a complementary copy (positive copy for negative stranded RNA and vice versa). sequencing facility role RBS:rbs A sequencing laboratory role is a laboratory role played by a population that performs the assay process of nucleotide or amino acid sequenceing analysis. MC, 08092009: moved as subclass of new mireoted term OBI_0000202, investigation agent role, which can be borne by either individuals or insitutions influenza virion MC, 20100212: submitted tracker item to IDO at http://code.google.com/p/infectious-disease-ontology/issues/detail?id=25 to clarify definition of parent term virion influenza assembled virus person: Melanie Courtot WEB: http://www.medterms.com/script/main/art.asp?articlekey=11558 influenza virus particle A complete virus particle of influenza virus with its DNA or RNA core and protein coat as it exists outside the cell. influenza hemagglutinin Influenza hemagglutinin is a type of hemagglutinin found on the surface of the influenza viruses. It is an antigenic glycoprotein. It is responsible for binding the virus to the cell that is being infected. WEB: http://en.wikipedia.org/wiki/Hemagglutinin_%28influenza%29 MC, 20101201: added as subclass of hemagglutinin person: Melanie Courtot Influenza haemagglutinin 20100203: submitted to PRO: http://sourceforge.net/tracker/?func=detail&atid=1135711&aid=2945554&group_id=266825 neuraminidase Neuraminidase enzymes are glycoside hydrolase enzymes (EC 3.2.1.18) that cleave the glycosidic linkages of neuraminic acids. Neuraminidase enzymes are a large family, found in a range of organisms. The most commonly known neuraminidase is the viral neuraminidase, a drug target for the prevention of influenza infection. The viral neuraminidases are frequently used as an antigenic determinants found on the surface of the Influenza virus. Some variants of the influenza neuraminidase confer more virulence to the virus than others. Neuraminidases, also called sialidases, catalyze the hydrolysis of terminal sialic acid residues from the newly formed virions and from the host cell receptors.[2] Sialidase activities include assistance in the mobility of virus particles through the respiratory tract mucus and in the elution of virion progeny from the infected cell.[3][4] person: Melanie Courtot MC, 20101202: added definition 20100203: submitted to PRO: http://sourceforge.net/tracker/?func=detail&aid=2945634&group_id=266825&atid=1135711 WEB: http://en.wikipedia.org/wiki/Neuraminidase virus isolation PERSON: Melanie Courtot WEB: http://virology-online.com/general/Test1.htm a material separation to recover the virusfraction of an input material haemadsorption Influenza and parainfluenza viruses do not ordinarily induce CPE, however they possess haemagglutinins and thus the ability to absorb guinea pig RBCs as they bud from the cell. This phenomenon is known as haemadsorption. Commonly employed cell cultures include primary monkey kidney, LLC-MK2 and MDCK cells. The cell cultures are incubated with a suspension of guinea pig RBCs at 4oC or RT for 30 minutes. The unabsorbed RBCs are then removed and the cell sheet observed microscopically for the presence of haemadsorption. PERSON: Melanie Courtot WEB: http://virology-online.com/general/Test1.htm the absorption of red blood cells by haemagglutinins viral isolate GenBank submission event URL:http://www.ncbi.nlm.nih.gov/Genbank/ A data transformation event that encompasses the process of submitting new or updated sequence information or annotation to GenBank. trypsin PERSON: Melanie Courtot Submitted to PRO, see https://sourceforge.net/tracker/?func=detail&atid=1135711&aid=3397087&group_id=266825 Trypsin (EC 3.4.21.4) is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins. Trypsin is produced in the pancreas as the inactive proenzyme trypsinogen. WEB: http://en.wikipedia.org/wiki/Trypsin disease severity URL:http://www.nationalasthma.org.au/html/strategy/camia/camia002.asp A disease phenotype that descrives the inherent severity of the disease independent of its management, including drug and other interventions. tissue culture infectious dose 50 URL:http://aleffgroup.com/AVISFMD/A010-fmd/mod2/0550-karber.html MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum TCID50 The quantity of virus in a specified suspension volume (e.g., 0.1 ml) that will infect 50% of a number (n) of cell culture microplate wells, or tubes trypsin auxotrophic organism An organism that requires tryspin to grow PERSON: Melanie Courtot immature URL:http://elibrary.unm.edu/sora/JFO/v017n01/p0027-p0033.pdf A bird after completing the post-juvenal molt, but has not acquired the complete adult plumage. A life stage of any bird older than a nestling or chick that has not reached sexual maturity or its basic winter or first winter plumage. cough SYMP:614 URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=cough An explosive expulsion of air from the lungs acting as a protective mechanism to clear the air passages or as a symptom of pulmonary disturbance. intensity of body moult A intensity of body moult is a measurement datum that describes the intensity of the periodic replacement of epidermis (skin), pelage (hair, fur, wool), or other external layer. In some species, other body parts may be shed, for example, wings in some insects. Examples include old feathers in birds, old hairs in mammals (especially dogs and other canidae), old skin in reptiles, and the entire exoskeleton in arthropods. http://en.wikipedia.org/wiki/Moult 20110823, MC: need to check on the unit for this. If it has a unit it should be asserted under scalar measurement datum 20110823: this term initially refered only to bird in its definition. We may also need to create a moulting process. virus passage date FLU:MK Date that the virus passage(s) took place. annotation event URL:http://www.ncbi.nlm.nih.gov/projects/genome/guide/E132 An annotation event is a data transformation event which encompasses adding biological information to genome sequence. This is a very complex task, and the process for doing this is rapidly evolving. Several groups are doing automated computational annotation of several genomes. Features that are added to the genome often include gene models, SNPs, and STSs. GenBank name GenBank notes collection latitude GPS GROUP: FLU The GPS latitude coordinate where the sample was collected. data about a laboratory RBS:rbs MC, 20101118: this is a placeholder meant to be removed when we will have a laboratory, which will allow us to define current subclass using the is_about relation MC, 08092009: moved from quality to GDC. Those are information entities. Need additional clean up. There is no laboratory role. MC, 20101118: moved under data item and renamed data about a laboratory from "quality of a laboratory" Those should be outsourced towards the organization ontology. neuraminidase typing URL:http://www.springerprotocols.com/Full/doi/10.1007/978-1-59745-279-3_8?encCode=REZJOjhfMy05NzItNTQ3OTUtMS04Nzk=&tokenString=ycLy0AkcLqNgMccOI6y30w== An assay which aims at determining the neuraminidase type of an influenza virus. N typing juvenile URL:http://elibrary.unm.edu/sora/JFO/v017n01/p0027-p0033.pdf A young bird out of the nest and able to take care of itself, but which has not completed the post-juvenal molt. initial oxygen saturation URL:http://gyre.umeoce.maine.edu/data/gomoos/buoy/doc/buoy_system_doc/buoy_system/g6572.html MC, 20101119: moved from quality to scalar measurement datum. Initial oxygen saturation is a scalar measurement datum that describes the initial volume of oxygen gas (STP) absorbed from humidity-saturated air at a total pressure of one atmosphere, per unit volume of the liquid at the temperature of measurement (units ml/l). date URL:http://www.gnu.org/software/radius/manual/html_node/radius_36.html A date in the format: MON DD CCYY, where MON is the usual three-character abbreviation for month, DD is day of month (1-31), CCYY is the year, including the century. Date may also be reported as year CCYY. (DDMMYY). fledgling specimen identification number MC, 20101118: removed dbxref to PATO_0001226, count. Updated from "sample number" to "specimen identification number" as per Burke's use case GROUP: FLU The unique number inhering in and identifying the specimen fatigue MP:0002899 'Mammalian phenotype' SYMP:0019177 URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=fatigue Weariness or exhaustion from labor, exertion, or stress. myalgia SYMP:0000626 URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=myalgia Pain in one or more muscles. virus pathogenicity after passage URL:http://www.pnas.org/cgi/content/abstract/97/13/6974 virus passage level MC, 20101119: moved from quality of specimen to scalar measurement datum A scalar measurement datum denoting the pathogenicity of a virus after several passages in cell culture. MC, 20101201: updated definition and label collection province GROUP: FLU The name of the geographic province where the collection occurred. yearling Flu:ls A bird that was observed the summer following its year of hatch. sequence submission date FLU:MK Date that the sequence was submitted (i.e. to GenBank). GenBank district specimen collection date FLU:MK Calendar date that the specimen was collected. GenBank projected_timeline virus passage A virus passage is a transforming material transformation that involves the incubation of a pathogen (as a virus) in a tissue culture, a developing egg, or a living organism to increase the amount of pathogen or to alter its characteristics WEB:http://www.merriam-webster.com/medical/passage GenBank template_id vaccinated organism GROUP: FLU An organism which has been vaccinated vaccination status is an IA about a vaccinated host collection district GROUP: FLU The name of the district where the sample was collected. GenBank submission date sample quantity GROUP: FLU PATO:0001226 MC, 20101118: moved from specimen quality to scalar measurement datum The sample amount as measured in grams, milliliters or other standard unit of measurement. RNA extraction protocol viral RNA extraction PERSON: Melanie Courtot A RNA extraction from a virus primaries flight feather URL:http://volusia.org/birding/glossary.htm Large outermost flight feathers on wing. Can vary from 9-11, but the number remains constant within a species. collection country GROUP: FLU The name of the country where the sample was collected. lethal dose 50 URL:http://www.virology.net/ATVGlossary.html MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum The measure that describes the dosage of a drug or poison that is toxic to 50% of the organisms it is tested against. specimen collector role A specimen collector role is a study personnel role that is performed by a erson who collects the specimen from the environment. strain taxonomy name URL:http://www.niwa.cri.nz/rc/freshwater/fishatlas/glossary MC: 20101119: moved from strain specimen quality to label. Not sure this term is required. The taxonomic name for a strain species, consisting of two words, the genus and species. secondaries flight feather URL:http://volusia.org/birding/glossary.htm Flight feathers, smaller than the primaries, occurring in series along rear edge of wing between scapulars, inward of primaries. GenBank subtype URL:http://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html The subtype is a quality that describes the subtype of organism from which sequence was obtained. rural environment URL:http://en.wiktionary.org/wiki/rural 20110826, MC: renamed from "rural" to "rural environment". Moved under environment. Rural environment is an environment that is characterized by sparsely-populated non-urban areas, such as found in farming communities or the countryside. sequence coverage wiki:http://en.wikipedia.org/wiki/Shotgun_sequencing Sequence coverage is the average number of reads representing a given nucleotide in the reconstructed sequence. It can be calculated from the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G. For example, a hypothetical genome with 2,000 base pairs reconstructed from 8 reads with an average length of 500 nucleotides will have 2x redundancy. This parameter also enables one to estimate other quantities, such as the percentage of the genome covered by reads (sometimes also called coverage). MC, 20101201: old definition was "A sequencing specification that describes the average number of times a nucleotide position was sequenced to obtain a consensus." Moved from sequencing specification to measurement datum virus passage history record URL:http://www.pnas.org/cgi/content/abstract/97/13/6974 virus passage number A virus passage history record is a passage history record that details the number of times a virus has been passaged in cell culture. MC, 20111123: moved from quality of specimen to passage history record, and renamed accordingly (with addition of alt term) Genbank reject date nucleic acid sequence has been scheduled for inclusion in OBI: nucleic acid sequence: A data item that is is a string of characters (e.g., A, G, C,T, U, N, R, Y, etc.) and represents the order of nucleotides found somewhere in nature or synthesized. sequence submitter role RBS:rbs A sequence submitter role is a study personnel role that is repsponsible for sending sequence (DNA, RNA, Protein) data to a repository, usually GenBank. collection sub-district GROUP: FLU The name of the sub-district where collection occurred. sequencing protocol MC, 20101201: updated label from sequencing specification to sequencing protocol to match position in hierarchy A protocol which specifies conditions, parameters and instructions to be used when performing sequencing assays PERSON: Melanie Courtot GenBank length wiki:http://en.wikipedia.org/wiki/Length The length is a quality that describes measure of the nucleotide or amino acid sequence from beginning to end. GenBank prep_date transmission environment FLU:MK 20110826, MC: trasnformed into a defined class. Subclasses rural and urban were renamde and asserted under environment A transmission environment is the environment in which the etiologic agent was harbored and spread from host to host. extraction date FLU:MK Calendar date that the sample was extracted. lab isolation date FLU:MK Date that the laboratory isolated the sample. viral replication titer URL:http://www.springerprotocols.com/Full/doi/10.1007/978-1-59745-279-3_8?encCode=REZJOjhfMy05NzItNTQ3OTUtMS04Nzk=&tokenString=ycLy0AkcLqNgMccOI6y30w== MC, 20101119: updated label from "replication titer" to "viral replication titer" MC, 20101119: moved from quality to scalar mesurement dtum and updated defintiion accordingly A scalar measurement datum that denotes the virus replication level. mature URL:http://www.dfw.state.or.us/resources/hunting/upland_bird/projects/mtn-quail.asp A bird after hatch year. bird wing length unflattened GROUP: FLU MC, 20101118: moved from winged organism anatomy to length measurement datum The measured length of the bird wing as the wing is held without being flattened. throat pain SYMP:505 URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=sore%20throat Painful throat due to inflammation of the fauces and pharynx. egg infectious dose 50 :1938. L. Reed and H. Muench MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum A strain specimen phenotype that describes the egg infectious dose 50 amount of a virus which is required to kill 50% of the eggs. GenBank accession URL:http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/genejargon.shtml An accession number is a quality that describes the unique identifier assigned to the entire sequence record when the record is submitted to GenBank. environment GROUP: FLU MC, 20101202: moved under site and definition updated from "An environment is a spatial region having environmental qualities which may sustain an organism or a community of organisms." An environment is a site having environmental qualities which may sustain an organism or a community of organisms. nucleotide sequencer role A nucleotide sequencer role is a study personnel role that is performed by a person who determines the genetic sequence for a biomateral. data about a collection location MC, 20101118: this is a placeholder meant to be removed when we will have the collection process, which will allow us to define current subclass using the is_about relation MC, 20101118: renamed from collection location context organism treated with antibiotics 20110824, MC: renamed from "antibiotics administered" after adding correct restrictions. Note that even thought we say "organism treated with antibiotic" the sense of treated is not the one from OGMS:treatment - there doesn't have to be therapeutic intent. An organism which has been treated with antibiotics bird length head to beak GROUP: FLU MC, 20101118: moved from winged organism anatomy to length measurement datum The measured length from the birds head to beak. genbank virion RNA submission event MC, 20101207: I am trying to say logically that the info submitted is about the RNA sequence that has been obtained by sequencing the RNA that had been extracted from the virion A GenBank submission event in which the RNA sequence of a virion is submitted PERSON; Melanie Courtot hemagglutinin titer URL:http://www.virology.net/ATVGlossary.html A measure of the amount or concentration of hemagluttanin in solution. MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum bird beak length GROUP: FLU MC, 20101118: moved from winged organism anatomy to length measurement datum The measured length of the birds beaks. runny nose SYMP:0000372 URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=Rhinorrhea Excessive mucous secretion from the nose. fever GO:0001660 'Gene ontology' SYMP:613 URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=fever A rise of body temperature above the normal whether a natural response (as to infection) or artificially induced for therapeutic reasons. nestling URL:http://elibrary.unm.edu/sora/JFO/v059n03/p0235-p0238.html A young bird confined to the nest. Nestlings are infant birds having little or no feathering. They may be pink and naked, covered with down feathers, or covered with needle-like feathers (called pin feathers). sample name MC: 20101119: moved from strain specimen quality to label. Not sure this term is required. extraction time FLU:MK A defined period when the sample was extracted. GenBank lot laboratory address URL:http://www.gnu.org/software/radius/manual/html_node/radius_36.html The address that describes the physical (geographic) location of the laboratory facility. RNA amount shipped for sequencing PERSON: Melanie Courtot The amount of RNA that has been sent to the lab for sequencing purposes MC, 20101201: added definition for this term. Not sure how to deal with it though. plaque forming units per size URL:http://en.wikipedia.org/wiki/Plaque_forming_units MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum A plaque forming unit per size is a measure that is used in the assessment of the concentration of viruses in a sample. GenBank modification date collection city URL:http://www.epa-echo.gov/echo/case_report_dd.html The name of the city, town, or village where the sample was collected. GenBank created_by_person/group GenBank origin_lab bird wing length flat GROUP: FLU MC, 20101118: moved from winged organism anatomy to length measurement datum The measured length of the bird wing as the wing is held flat. collection longitude GPS GROUP: FLU The GPS longitude coordinate where the sample was collected. specimen collection protocol GROUP: FLU MC, 20101203: updated sample to specimen The protocol specifying how to collect the specimen hatch year Flu:ls A bird in the first year after hatching. hemagglutinin typing URL:http://www.springerprotocols.com/Full/doi/10.1007/978-1-59745-279-3_8?encCode=REZJOjhfMy05NzItNTQ3OTUtMS04Nzk=&tokenString=ycLy0AkcLqNgMccOI6y30w== An assay which aims at determining the hemagglutanin subtype of an influenza virus. HA typing MC, 20101202: made it a defined class as there are several methods to identify the heagglutinin type as per http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T32-4C47KNC-5&_user=1022551&_coverDate=07%2F31%2F2004&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1565330571&_rerunOrigin=google&_acct=C000050484&_version=1&_urlVersion=0&_userid=1022551&md5=c5d1a3bc08abe655acb70076b13e3a74&searchtype=a The haemagglutination-inhibition assay that is routinely used for subtyping and antigenic characterisation of influenza strains does not distinguish between A(H1N1) and A(H1N2) strains; therefore, alternative tests are required for typing the NA. The standard test used to determine neuraminidase type is a rather cumbersome and time-consuming procedure (approximately 18 h) which relies on inhibition, by antibody, of n-acetyl neuraminic acid release from a substrate such as fetuin (Aymard-Henry et al., 1973). Alternative methods of neuraminidase assay have been described, one for example relying on the agglutination of neuraminidase-treated erythrocytes by lectins (Fiszon and Hannoun, 1990 B Fiszon and C Hannoun, Comparison of neuraminidases of the same subtype but from different species using a new method of titration, J. Virol. Methods 27 (1990), pp. 79–90. Abstract | PDF (587 K) | View Record in Scopus | Cited By in Scopus (4)Fiszon and Hannoun, 1990) laboratory name wiki:http://en.wikipedia.org/wiki/Laboratory The name of the laboratory conducting the scientific research, experiments, analysis or sequencing may be performed. nasal congestion A nasal congestion is a symptom that is characterized by the blockage of the nasal passages usually due to membranes lining the nose becoming swollen from inflamed blood vessels. stuffy nose influenza virus antigenic data MC, 20101130: "Antibodies against the viral surface glycoprotein hemagglutinin (HA) provide protective immunity to influenza virus infection, and this protein is therefore the primary component of influenza vaccines. However, the antigenic structure of HA has changed significantly over time, a process known as antigenic drift (6), and in most years, the influenza vaccine has to be updated to ensure sufficient efficacy against newly emerging variants (7, 8). The World Health Organization coordinates a global influenza surveillance network, currently consisting of 112 national influenza centers and four collaborating centers for reference and research. This network routinely characterizes the antigenic properties of influenza viruses using a hemagglutination inhibition (HI) assay " MC, 20101130: renamed antigenic data (from strain antigenic data) and moved under data item from strain specimen quality Data reflecting the antigenic properties of influenza viruses characterized using a hemagglutination inhibition (HI) assay WEB: http://www.sciencemag.org/content/305/5682/371.full sequence annotator role Flu:ls The sequence annotator role is a study personnel role of a scientist who assigns a set of characteristics to a sequence for the purpose of documenting relevant infromation from experimental results to aid in their interpretation. Genbank isolation source extractor role A extractor role is a study personnel role that is performed by a person who extracts genetic material from a biomaterial. viral RNA segment person: Melanie Courtot RNA molecule constituting the genome of viruses vRNA segment principal investigator role OBI:0000103 A person with the lead role on the project, as a scientist or engineer. GenBank size treatment event MC, 20101207: I believe this term reflects the biochemical treatment of a sample and is therefore not equivalent to ogms: treatment which is a treatment to alleviate a disorder collection location name GROUP: FLU The name of the place where the sample was collected. laboratory tracking number PERSON: Melanie Courtot MC, 20101119: moved from "data about a laboratory" to "specimen identification nmber". See http://groups.google.com/group/influenza-ontology/browse_thread/thread/91adb05b5e6b80aa?hl=en A laboratory specimen tracking number is a specimen identification number assigned to a specimen by a laboratory with the objective to uniquely identify and follow the specimen. antiviral treatment date FLU:MK Calendar date that antiviral treatment was administered. GenBank center_project onset date GROUP: FLU Date when host first experienced clinical symptoms. MC, 20101119: moved from quality>output assessment > measure to date collection time FLU:MK A defined period when the sample was collected. GenBank gi URL:http://www.ncbi.nlm.nih.gov/Class/FieldGuide/glossary.html#G A GI number is a quality that is an identifier assigned to all sequences at the NCBI, which points to a specific version of a sequence record. GI stands for GenInfo, a database system at NCBI that preceded the Entrez system. collection quantity A collection quantity is a generically dependant continuant that specifies the quantity of material collected. life stage PATO:0000261 virus isolation protocol GROUP: FLU Method by which virus is isolated. quality of organism GenBank lib_name collection state GROUP: FLU The name of the state where the collection occurred. sequence received date FLU:MK Date that the laboratory received the sequence. genomic sequencing MC, 20101207: we can't say that the output information is about the input material MC, 20101207: moved under DNA sequencing MC, 20101207: I think genomic sequencing is an assay that has specified input some DNA (genome?) and has specified output some genotype or ICE about a sequence urban environment URL:http://wordnet.princeton.edu/perl/webwn?s=urban 20110826, MC: renamed from "urban" to "urban environment". Moved under environment. Urban environment is an environment that is characterized by densely-populated areas, such as found in cities. human social group URL:en.wiktionary.org/wiki/social group A human social group is a material entitiy that is a collection of humans, who share certain characteristics, interact with one another, accept expectations and obligations as members of the group, and share a common identity. amplification protocol headache SYMP:504 URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=headache A pain in the head. organism treated with antiviral drug An organism which has been treated with antiviral drugs. extraction protocol hospitalized host A host hospitalized is a condition that indicates whether or not an organism has been hospitalized. GenBank bac_name URL:http://www.ncbi.nlm.nih.gov/Class/FieldGuide/glossary.html#B A bac_name is a quality that identifies the bacterial artifical chromosome (bac), a large insert cloning vector capable of handling large segments of cloned DNA, typically around 150 kb, which are used in the construction of genomic libraries for genome scale sequencing projects including human, mouse, Arabidopsis, and rice. bird band identification number A bird band identification number is a number identifies the individual (often the host) - analagous to a name in a human. GROUP: FLU MC, 20101118: moved from quality of organism to identification number antiviral treatment URL:http://www.cdc.gov/flu/professionals/antivirals/indications.htm A treatment that specifies which, if any, antiviral treatment has been administered to a host. data about a genbank entry MC, 20101118: renamed "data about a genbank entry" from "qualities of genbank" and moved under data item. We should create a genbank record and use the is_about relation to link both MC, 20101118: this is a placeholder meant to be removed when we will have the class "genbank entry", which will allow us to define current subclass using the is_about relation MC, 08092009: those need clean up ligated ends molecule A ligated ends molecule is a biological macromolecule with overhanging nucleotides that assist in the ligation process. MC, 20101118: moved under processed material and updated definition post disease onset sample collection period GROUP: FLU The time period that comprises the sample collection period when the sample was collected following the disease onset. adult URL:http://www.okaponds.com/tips.htm A bird with definitive plumage or sexually mature. Adult birds are mature, independent birds who are fully feathered for flight and capable of surviving on their own (in regards to food, shelter, etc. duration of illness GROUP: FLU MC, 20101123: moved from quality of infectious disease to duration The number of days the patient was ill. specimen barcode A specimen barcode is a specimen identification number formatted as an optical machine-readable representation. PERSON: Melanie Courtot WEB: http://en.wikipedia.org/wiki/Barcode MC, 20101118: moved from "quality of specimen" under specimen identification number. antibody titer A antibody titer is output of a measurement that describes the measure of antibodies in a biomaterial. passage history record See http://groups.google.com/group/influenza-ontology/browse_thread/thread/12b3fb5ef0501b5b?hl=en A passage history record is a data item recording in sequential order the hosts in which the strain has been previously subcultured in. PERSON: Burke Squires PERSON: Melanie Courtot bird identification band A plastic or metal ring attached usually to the ankle of the bird and bearing a band identification number MC, 20101201: added as bearer of band identification number as per Burke's email at http://groups.google.com/group/influenza-ontology/msg/8781d389ec670463?hl=en hemagglutination disposition A disposition to initiate an hemagglutination process PERSON: Melanie Courtot hemagglutinin PERSON: Melanie Courtot WEB: http://en.wikipedia.org/wiki/Hemagglutinin MC, 20101201: added as request to PRO tracker unanswered. See http://sourceforge.net/tracker/?func=detail&aid=2945554&group_id=266825&atid=1135711 Hemagglutinin is a substance that causes red blood cells to agglutinate (has disposition hemagglutination) enrichment process the process of increasing the concentration of a particule of interest in a sample PERSON: Melanie Courtot antiviral drug A drug used specifically for treating viral infections. PERSON: Melanie Courtot WEB: http://en.wikipedia.org/wiki/Antiviral_drug virus amplification A material processing aiming at increasing the number of viruses in a specimen PERSON: Melanie Courtot neuraminidase inhibitor PERSON: Melanie Courtot The function of inhibiting the viral neuraminidase protein, thus preventing the virus from reproducing by budding from the host cell. WEB: http://en.wikipedia.org/wiki/Neuraminidase_inhibitor influenza neuraminidase A type of neuraminidase found on the surface of influenza viruses that enables the virus to be released from the host cell. MC, 20101202: When influenza virus replicates, it attaches to the cell surface using hemagglutinin, a molecule found on the surface of the virus which binds to sialic acid groups. Sialic acids are found on various glycoproteins at the host cell surface, and the virus exploits these groups to bind the host cell. In order for the virus to be released from the cell, neuraminidase must enzymatically cleave the sialic acid groups from host glycoproteins. As an integral part of influenza replication, blocking the synthesis of neuraminidase with neuraminidase inhibitors is an effective way to treat influenza. PERSON: Melanie Courtot WEB: http://en.wikipedia.org/wiki/Viral_neuraminidase neuraminidase inhibitor drug A drug targeted at the influenza virus, which work by blocking the function of the viral neuraminidase protein, thus preventing the virus from reproducing by budding from the host cell. PERSON: Melanie Courtot WEB: http://en.wikipedia.org/wiki/Neuraminidase_inhibitor specimen collection PERSON: Melanie Courtot MC, 20101203: added this class to realize the concretization of the collection protocol the process of collecting a specimen, either from an organism or from an environment isolation event