I ran into a problem loading the attributes, so the new attribute system is still offline; however, I have a list of the keys and my attempt at a description of what each one means. They are arranged in a table below the fold.
Please let me know if I am describing any of the attributes incorrectly.
| Key | Type | Description | Groups |
|---|---|---|---|
| BS essential Kobayashi | text | Essentiality of a Bactillus Subtilis gene as determined in the paper by Kobayashi, et al, PMID 12682299, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| Biotype | string | Type of biological variance used to distinguish an organism's strains, such as pathological target (pathovar) or biological characteristics (biovar). | Genome |
| CMR ID | string | Clinical Microbiology Review number for a genome. | Genome |
| CMR alias | string | Alphanumeric code for a genome in the Clinical Microbiology Review. | Genome |
| Chromosome Type | string | Shape of the chromosomes for a genome: linear, circular, or spirochete. | Genome |
| Comment | text | General comment about the status of a genome, subsystem, or feature. | Feature, Genome, Subsystem |
| Contact | string | HTML for contacting the person or organization responsible for a genome, feature, or subsystem, usually encoded as text with a "mailto" hyperlink. | Feature, Genome, Subsystem, hyperlinked |
| DomainType | string | Domain type structure for a bacteria genome (e.g. Phage). | Genome |
| Doubling Time Mins | int | Number of minutes it takes a population of an organism to double. | Genome |
| Doubling Time Range | string | Description of how long it takes an organism population to double. | Genome |
| EC contribute to fitness | text | Essentiality of an Escherichia Coli gene as determined in the paper by Gerdes et al, PMID 13129938, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| NC number | string | NC number (locus) for a genome in the NCBI nucleotide database. | Genome |
| EC essential Blattner | text | Essentiality of an Escherichia Coli gene as determined by the University of Wisconsin mutagenesis ORF mapping project, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| EC essential Keio | text | Essentiality of an Escherichia Coli gene as determined in the paper by Baba et al, PMID 16738554, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| EC essential Shigen | text | Essentiality of an Escherichia Coli gene as determined by the PEC database, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| Funding | string | HTML for a genome or subsystem's funding source, generally encoded as a name hyperlinked to an institution's home page. | Genome, Subsystem, hyperlinked |
| Genome Database | text | HTML for a genome's database entries, generally encoded as a list of names, each hyperlinked to a database web page. | Genome, hyperlinked |
| Gram stain | string | Indication of whether a bacteria genome is gram-positive or gram-negative. | Genome |
| has essentiality data | string | Indicates that essentiality data exists for a genome. | Genome |
| HP candidate essential Salama | text | Essentiality of a Helicobacter pylori gene as determined in the paper by Salama et al, PMID 15547264, encoded as a rating and a URL. | Feature, essential, url associated |
| Habitat | string | Habitat in which this organism appears, such as Soil, Shallow water, Human skin, Animals, and so forth. | Genome |
| Institution | text | HTML listing the institutions at which an organism is studied, generally encoded as a list of names, each hyperlinked to the institution home page. | Genome, hyperlinked |
| Length | float | Length of a genome, in megabases. (See also the "Size" attribute.) | Genome |
| Links | text | HTML listing of links related to a genome, feature, or subsystem, generally encoded as a list of page names, each hyperlinked to the appropriate page. | Feature, Genome, Subsystem, hyperlinked |
| MG contribute to fitness Hutchison | text | Essentiality of a Mycoplasma genitalium gene as determined in the paper by Hutchinson et al in Science magazine, Vol. 286. no. 5447 (1999), encoded as a rating and a URL. | Feature, essential, peg, url associated |
| MG essential Hutchison 2006 | text | Essentiality of a Mycoplasma genitalium gene as determined in the paper by Glass et al, PMID 16407165, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| MT contribute to fitness Rubin | text | Essentiality of a Mycobacterium tuberculosis gene as determined in the paper by Sassetti et al, PMID 12657046, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| Motile | string | Motility of the specified organism. | Genome |
| NCBI Genome Numbers | string | ID numbers of a genome in the NCBI Genome Database, encoded as a comma-separated list of numbers. | Genome |
| NC URL | text | HTML text for displaying a genome's description on the NCBI web site, generally encoded as an NC number hyperlinked to the appropriate web page. | Genome, hyperlinked |
| Notable Features | text | Useful things to know about a genome that do not fit in any other category. | Genome |
| Number of Bacteriophage | counter | Number of bacteriophage insertions in a genome. | Genome |
| Number of Chromosomes | counter | Number of chromosomes in a genome. | Genome |
| Number of Megaplasmids | counter | Number of megaplasmids in a genome. | Genome |
| Number of Plasmids | counter | Number of plasmids in a genome. | Genome |
| Order Of Publication | counter | Ordinal position of a genome in terms of when it was added to the data store. | Genome |
| PA candidate essential Jacobs | text | Essentiality of a Pseudomonas aeruginosa gene as determined in the paper by Jacobs et al, PMID 14617778, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| PA essential PA14 PAO1 Liberati | text | Essentiality of a Pseudomonas aeruginosa gene as determined in the paper by Liberati et al, PMID 16477005, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| PIRSF | text | SF classification for a gene in the Protein Information Resource database, encoded as descriptive text and a URL. | Feature, peg, url associated |
| PUBMED | text | PMID for a paper relating to a gene, encoded as a number and a URL. | Feature, pubmed, url associated |
| Publication | text | Publication reference for a genome or feature, encoded as a description and a URL. | Feature, Genome, pubmed, url associated |
| Publication Date | string | Year in which a genome was published. | Genome |
| Publication | string | Indication that a genome, subsystem, or feature is unpublished, but publication is in progress. | Feature, Genome, Subsystem |
| SA essential Forsyth | text | Essentiality of a Staphlococcus Aureus gene, as determined in the paper by Forsyth et al, PMID 11952893, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| SA essential Ji | text | Essentiality of a Staphlococcus Aureus gene, as determined in the paper by Ji et al, PMID 11567142, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| SA essential merged Forsyth and Ji | text | Essentiality of a Staphlococcus Aureus gene, as determined in the paper by Ji et al, PMID 11567142, and Forsyth et al, PMID 11952893, encoded as a rating only. | Feature, essential, peg |
| SP essential Song | text | Essentiality of a Streptococcus Pneumoniae, as determined in the paper by Song et al, PMID 15995353, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| SP essential Thanassi | text | Essentiality of a Streptococcus Pneumoniae gene, as determined in the paper by Thanassi et al, PMID 12136097, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| SP essential merged | text | Essentiality of a Streptococcus Pneumoniae gene, as determined in any of the papers used, encoded as a rating only. | Feature, essential, peg |
| ST essential Knuth | text | Essentiality of a Salmonella Typhimurium gene, as determined in the paper by Knuth et al, PMID 15009898, encoded as a rating and a URL. | Feature, essential, peg, url associated |
| Secondary Habitat | string | Alternative habitat for a genome. | Genome |
| Serotype | string | Variance type for genome strains based on the cell surface. | Genome |
| Shape | string | Physical shape of a unicellular genome. | Genome |
| Size | text | Length of a genome, encoded as descriptive text with an optional hyperlink to a gene map. (See also the "Length" attribute.) | Genome, hyperlinked |
| Status | string | Status of a genome: complete or incomplete. | Genome |
| Temperature | int | Optimal operating temperature for a genome, in degrees Celsius. | Genome |
| Total Replicons | int | Number of replicons for a genome. | Genome |
| Width | float | Width of a genome cell, in nanometers. | Genome |
| extremophile | string | Indicates whether or not a genome prefers extreme environments, generally either "No" or a comma-delimited list of the extremes ("hyperthermophilic", "acidophilic"). | Genome |
| evidence code | text | Evidence for an annotation, generally encoded as a code word and a description. | Feature |
| carbon | text | Indicates whether a genome uses organic or inorganic carbon. | Genome |
| cell surface | text | Indication that a feature creates a cell surface protein, generally encoded as a role abbreviation and a reference (URL or citation). | Feature, peg, url associated |
| disease | string | Indication of whether or not a genome causes a disease. | Genome |
| collection | string | Name of a collection containing a subsystem. A subsystem may be in more than one collection or in no collection. | Subsystem |
| established antibiotic inhibitor | text | Antibiotic inhibition properties of a PEG, encoded as a description and a URL. | Feature, peg, url associated |
| established antibiotic target | text | Indicates that a PEG is targeted by an antibiotic. Encoded as a description of the antibiotic and its role (e.g. "MurA, inhibited by phosphomycin"), and a URL. | Feature, peg, url associated |
| higher plants | string | Indicates that a genome is a high-order plant. | Genome |
| humans | string | Indicates whether or not a genome is found in humans. | Genome |
| iedb epitopelinearsequence | text | Protein subsequence that is used by antibodies to identify the parent organism, encoded as protein letter codes and a URL to the IEDB page. | Feature, iedb, peg, url associated |
| iedb epitopename | string | Name assigned by the IEDB for the protein subsequence that is used by antibodies to identify the parent organism. | Feature, iedb, peg |
| intracellular | string | Indicates whether or not a genome lives inside other cells. | Genome |
| microarray sigmaB regulon | text | Indication that a peg has been demonstrated in a microarray experiment to be regulated by the sigmaB stress transcription factor, generally encoded as a description ("up regulon" or "down regulon") and a URL. | Feature, peg, url associated |
| mouse passage in THY 18 hours change | text | Indication of how a gene's protein passes through mouse skin in a Todd-Hewitt yeast broth after 18 hours, generally "up", "down", or "no change". | Feature, peg |
| obligate | string | Indication of whether a genome is an obligate parasite, generally encoded as "yes", "no", or "free-living". | Genome |
| oxygen | string | Indication of whether a genome uses oxygen, generally encoded as "aeorobic", "anaerobic", "facultatively anaerobic", or "microaerophilic". | Genome |
| pH | string | pH for a genome's optimal environment, generally encoded as a number or a number and a month. | Genome |
| pH Range | string | Description of the pH range of a genome's survivable environment. | Genome |
| pH 75 vs 55 | text | Indication of how a gene expression is affected by a drop in environmental pH from nearly neutral to mildly acidic, encoded as a regulation effect ("up regulated" or "down regulated") and a URL. | Feature, peg |
| ralp3 mutant in THY 18 hours change | string | Indication of how a gene is affected by the mutated RALP3 regulon after 18 hours of a Todd-Hewitt Yeast broth, generally encoded as "up", "down", or "no change". | Feature, peg |
| ralp3 mutant in THY OD4 change | string | Indication of how a gene is affected by the mutated RALP3 regulon after exposure to oligodextran IV in a Todd-Hewitt Yeast broth, generally encoded as "up", "down", or "no change". | Feature, peg |
| secreted protein signal | string | Indication of how the secreted protein signal of a PEG was deduced, generally encoded as an underscored phrase such as "secreted protein by neural network" or "uncleavable signal by hidden markov model", among others. | Feature, peg |
| structure | string | Description of how the structure of a peg's protein was deduced, along with a URL to the protein's entry in the SCOP database. | Feature, peg, url associated |
| toxin | text | Indication that a peg's protein is a toxin, generally encoded as a descriptive phrase ("alpha-hemolysin precursor, alpha hemolysin") and a URL. | Feature, peg, url associated |
| vector | string | Transmission vector for a pathogen (e.g. "fleas", "airborne") | Genome |
| virulence associated | text | Indication that a PEG is associated with virulence, generally encoded as a description of how the virulence was determined and a URL. | Feature, peg, url associated, virulent |
| virulence associated by Rot expression analysis | text | Indication that a PEG is associated with virulence as determined by analysis of toxin supressors, generally encoded as the feature's identification in the source paper alias and a URL. | Feature, peg, url associated, virulent |
| virulence associated by adhesion properties of mutants | text | Indication that a PEG is associated with virulence as determined by fibronectin-binding of the expressed protein, generally encoded as a description and a URL. | Feature, peg, url associated, virulent |
| virulence associated by mutagenesis and nematode killing | text | Indicates that virulence is associated with this gene, as determined by experiments in which mutated organisms are tested for lethality in nematode worms, generally encoded as a protein name, a descriptive phrase, and a URL. | Feature, peg, url associated, virulent |
| virulence associated by evolution of epidemic microarray | string | Indication that a PEG is associated with virulence as determined by microarray data on evolution of the parent genome, generally encoded as the name of the feature in the source paper and a URL. | Feature, peg, url associated, virulent |
| virulence associated by screening mutants in murine model | text | Indicates that virulence is associated with this gene, as determined by experiments in which mutated organisms are tested with a murine model, generally encoded as a protein name, an author name, and a URL. | Feature, peg, url associated, virulent |
| virulence associated by site specific mutation | text | Indicates that virulence is associated with this gene, as determined by experiments in which organisms are mutated at a specific site, generally encoded as a protein name, an description, and a URL. | Feature, peg, url associated, virulent |
| virulence associated by vaccination | text | Indicates that virulence is associated with this gene, as determined by its effects on the expression of clumping factor A, generally encoded as a protein name, an description, and a URL. | Feature, peg, url associated, virulent |
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