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-{"file": "styleguide_NBK988/A255.nxml", "text": "Please let me know if any of the style points seem awkward to you. What works in one field may not be as useful in another. A style point is something that is decided upon by the person(s) in charge or by a committee (that decides to do something because of the historical use of doing something more one way than another or after analysis of the needs of all members of the group), but by whatever means agreement is reached for style points, the main use of style points is to improve consistency.\nPlease note: Styling of \nAppendices, Boxes, Figures, References, and Tables is in Special Content.\nAmino Acids\nThere are only four nucleotides (A, C, G, and T), but a sequence of three of the four nucleotides specifies an amino acid. The three nucleotides, sometimes called triplets, make up the codon.\nUse the three-letter abbreviations for amino acids in chains, as well as with codon numbers and mutations.\n\nExamples:\n\nArg-506\nArg506Gln\nMet-Phe-Val-Asn-Gln-His\n\nNote: Single-letter abbreviations should be used sparingly.\n\nExample:\n\nMFVNQH (instead of Met-Phe-Val-Asn-Gln-His)\n\nAmino acid abbreviations are determined by IUPAC.\nCapitalization\nSee CBE, pp. 149-165.\nNote: When a sentence begins with an abbreviation or designation that has an initial lowercase letter, the abbreviation or designation retains its lowercase.\n\nExample:\n\nOur study determined the protein to be p53. p53 has been studied extensively.\nCentrifugation\nUse g force (3000g), not rpm. Note that there is no \u201ctimes\u201d sign.\nColons\nAccording to CBE, there are four general uses of colons and nine specialized uses (pp. 44-46). Here, I will provide you with a few examples of the usual things.\n\nExample:\n\nNote: The images were scanned from photographs.\nIn the example above, note the capital \u201cT\u201d after the colon.\n\nExample (from atitle):\n\n2. LocusLink query terms: controlled terms.\nIn the example above, note the lowercase \u201cc\u201d after the colon.\n\nExample (from a Reference):\n\nAl-Shahrour F, Diaz-Uriarte R, Dopazo J. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics. 2004 Mar 1;20(4):578-80. Epub 2004 Jan 22.\nIn the example above, note the lowercase \u201ca\u201d after the colon.\n\nExample (from a Title):\n\nGenBank: The Nucleotide Sequence Database\nIn the example above, note the capital \u201cT\u201d after the colon.\nCommas\nRefer to CBE, pp. 48-52, for a complete discussion. The purpose of the comma is to make the sentence clear. It is not a symbol of conversational pause.\nIn general, use a \u201cserial comma\u201d to avoid ambiguity. A serial comma sets off a \u201csimple series of more than two elements\u201d (see the commas set in bold in the next example).\n\nExample:\n\nMIM is organized into autosomal, X-linked, Y-linked, and mitochondrial catalogs, and MIM numbers are assigned sequentially within each catalog.\nThe comma not set in bold in the example above is a comma used to separate independent clauses (complete sentences). This comma makes the sentence easier to read and understand.\nAnother comma error is the use of a comma between the subject and the verb. The separation of the subject from the verb by an intervening comma is called \u201ccomma separation\u201d.\n\nExample:\n\nWRONG: Suggested corrections and additions are welcome for future updates of these pages, and should be sent to the author.\nRIGHT: Suggested corrections and additions are welcome for future updates of these pages and should be sent to the author.\nConcentrations\nShow liter as \u201cl\u201d with combinations of units but written out as \u201cliter\u201d otherwise. Show gram as \u201cg\u201d (and kilogram as \u201ckg\u201d). Abbreviate mol/l as \u201cM\u201d.\nDashes\nThere are two types of dashes, the en dash (\u2013) and the em dash (\u2014). (A hyphen is shorter than an en dash.)\nen dash\nused to separate ranges and words of equal weight\n\nExamples:\n\n63\u201365, Mann\u2013Whitney, dose\u2013response curve\nem dash\nused to break a thought in a sentence (which is often a long pause, an aside, or a title fragment)\n\nExample:\n\nOnce he made the decision\u2014did I say that already?\u2014nothing stopped him from reaching his goal.\nContrast these uses with hyphens (see Hyphens).\nDecimal Points\nInsert 0 in numbers less than 1 (0.05).\nDegrees\nClose up symbol to number (55\u00baC).\nFor educational degrees, such as MD and PhD, do not use periods.\ne.g.\nUse to mean \u201cfor example\u201d. Do not italicize; use periods and follow with a comma.\nSee also Italics.\net al\nDo not italicize. Provide all names in the \u201cReferences\u201d section. In other formats (where the display of information is an issue because of space), reference citations may use et al. with only one author.\nSee also Italics.\netc\nSubstitution of \u201cand others\u201d or removal of the term is preferred, if possible.\nEmphasis\nUnderlining is not preferred for emphasis within the text to avoid confusion with underlining that is used to show Web links. (If hyperlinks are shown in a different color of underlining or in a different manner so that no confusion would exist, underlining for emphasis would be OK.)\nUse quote marks to show that a word is used in an unusual way. If emphasis if needed to show how an acronym was derived, use boldface letters for the beginning of each word, e.g., Deleted in Colorectal Carcinoma (DCC). When the derivation of the acronym is obvious, do not use the boldface letters. See also Voice: Active versus Passive.\nEquations\nIf equations are numbered, cite them as Equation 1, etc. Capitalize the word Equation and write it out in the text, figures, tables, and boxes. A sentence (or sentence fragment) introducing an equation ends with a colon. The equation itself does not receive any type of sentence punctuation, such as a period, semicolon, or comma, at its end.\nItalicize variables, but use roman type for SD, SE, CV, etc.\nSee also Math and Statistics.\nForeign Words\nSee Italics.\nGenes and Protein Designations\nGenes are italicized, and proteins are set in roman type (not italic). Use where reasonable. Web pages with long lists of genes in italics would be distracting. In this case, use roman type.\nHyphens\nHyphens are used for many purposes, such as with:\n\nprefixes and suffixescompound termscompound modifiers of several typesspelled-out fractionswritten-out forms of numbers from 21 through 99representation of single bonds in chemical or molecular formulas, peptide bonds in residues, and linkage of nucleotides\n\nprefixes and suffixes\ncompound terms\ncompound modifiers of several types\nspelled-out fractions\nwritten-out forms of numbers from 21 through 99\nrepresentation of single bonds in chemical or molecular formulas, peptide bonds in residues, and linkage of nucleotides\nSee CBE pp. 61-64 for many examples of the specific uses of hyphens. Below are a few common examples to make your search quicker.\nUnit Modifiers Are Hyphenated\ne.g., best-case scenario, false-positive results, high-risk behavior, model-fitted values\nNote\nTwo-word phrases that are easily understood as a unit are not hyphenated.\nNo Hyphen: amino acid residues\nUse a Hyphen with Some Prefixes\ne.g., anti-oncogenes, mis-segregation, non-redundant, pre-existing, BUT nonlinear, pretreatment\nMost \u201cco\u201d prefixes are closed up: coeluted, comigrate, copolymerize\nExceptions\nco-injected, co-worker\nCompounds with Phosphorus\nNo hyphen if the first word in the name is a noun. A group or adjectival form takes a hyphen, e.g., glucose 1-phosphate, cytosine 3[prime]-phosphate, glycerol-1-phosphate (see IUPAC-IUBMB).\nContrast hyphens with en dash and em dash (see Dashes). See also Amino Acids.\n-ical\nEnglish uses a couple of adjective endings that are sometimes confused: -ic and -ical. There are differences in meaning, and examples will best illustrate these differences.\nTake the pair of words classic/classical. You may own a classic car, but you listen to classical music. \u201cClassic\u201d refers to something being traditional and enduring, or serving as a standard of excellence\u2014perhaps an example of an outstanding model. \u201cClassical\u201d, on the other hand, refers to something that is a historically important form or genre of architecture, music, art, etc. Of the two forms, \u201cclassic\u201d seems to apply more to something specific, and \u201cclassical\u201d seems to apply to something broader, more general but distinguishable.\nConsider graphic/graphical. If you watch TV, you may see a lot of graphic violence, where \u201cgraphic\u201d more refers to the effects on the emotions, but if you choose, instead, to read The NCBI Handbook, you will be learning from its many graphical images, where \u201cgraphical\u201d more refers to the format of the material. Merriam-Webster's Dictionary does not make this particular distinction, so this is a style point. Here we are using \u201cgraphic\u201d to mean providing details of perhaps a shocking nature, whereas \u201cgraphical\u201d is used to mean a drawing, illustration, or art product.\ni.e.\nNote punctuation. Do not italicize.\nSee also Italics.\n\nin vitro, in vivo\nUse italics.\nSee also Italics.\nItalics\nThere are general and scientific uses of italics. On the use of italic and roman fonts for symbols in scientific text is available, as well CBE coverage on pages 169-171.\nFor our most common purposes, use italics for genus/species names, genes, loci, and alleles; parts of chemical names as appropriate (including cis, trans, ortho, meta, and para); all variables (e.g., probability (P or p)); and written-out Latin forms (such as a priori, ad libitum, de novo, in situ, in utero, in vitro, and in vivo).\nCBE considers whether a Latin word is common and suggests that \"in vitro\" and \"in vivo\" not be italicized. This, then, becomes a style point. I think it would be more confusing to selectively choose some written-out Latin words to be italic than to go along with the old standard of italicizing all of the Latin words.\nWhat of \u201ce.g.\u201d, \u201cet al.\u201d, \u201ci.e.\u201d, and \u201cetc.\u201d? Well, these are not written-out forms, AND they are very common; therefore, there is no need to italicize \u201ce.g.\u201d, \u201cet al.\u201d, \u201ci.e.\u201d, and \u201cetc.\u201d. More basically, the handling of Latin and other foreign words is influenced by the \u201cacceptance\u201d of a term as \u201ccommon\u201d as to whether an italic form is used. As specific foreign words become more common, the trend is for the italic style to be dropped, as a simplification. For example, uncommon French words used in English would still be shown in italics, but French words that have been used in English for a long time, such as \u201c\u00e0 la carte\u201d, are readily understood by most people and would not be set in italics (and some go so far as to drop the accent mark). Because differences of opinion can arise as to whether a foreign word has become common enough in English to go without italics, style points are then described in style guides, for the sake of consistency.\nWhen working with long lists of genus/species names, genes, loci, and alleles, particularly in tables, the italics become more of a distraction than a help for readers. In these cases, use your best judgment about the use of italics.\nPer changes by IUPAC in 2003, do not italicize the first three letters of restriction enzymes (EcoRI, BamHI).\nLatin\nSee Italics.\nLists\n\nParagraph format: Within paragraphs, use (a), (b), (c), etc. and then (i), (ii), (iii), etc.\n\nOutside of the paragraph format:\n\n\u2022 \u201cBulleted\u201d lists are fine. Be sure that all items with a similar weight use the same symbol.\nIn bulleted lists, entries of phrases, words, or sentence fragments do not use a period at the end of the entry. Do not connect list items with conjunctions such as \u201cand\u201d or \u201cor\u201d.\nIf the bulleted entries are complete sentences, use sentence capitalization and a period at the end of each entry.\n\u2022 Use a \u201cnumbered\u201d list only when the items must follow a sequence. When steps of a procedure are being referred to, use Arabic numbers (OK as a subsection within the bulleted list).\nFor more information, see Itemized Lists in Writing for the Web Environment.\nMath\nFollow CBE.\nNumbers/Numerals\nWrite out at the beginning of a sentence. Write out one to nine except with units of measure. Use numerals for 10 and above.\nNote: If a study is of 10 or more patients, items, things, etc., use numerals in sentences referring to parts of the total group, even when less than 10.\n\nExample:\n\nWe studied 36 patients. In the first group of 6 patients, only 2 were anemic.\nQuick List\nWritten-out numbers versus as numerals:\nFor numbers of 10 or more that do not refer to units of measure, use numerals.\nUnits of measure require numerals (3 mm, 4 months).\nAvoid beginning a sentence with a numeral.\nFractions: one-half, two-thirds, one-tenth, 1/32\nOrdinal numbers: 1st, 2nd, 3rd\nSeries: if the series contains numbers 10 or higher, use all numerals (3 mice, 4 rats, and 11 hamsters)\nEither side of the decimal point: use 0.1 not .1 (all cases); use 6.0 not 6 (only if significant)\nCommas: 3,000; 14,000; 3,333,331\nTime 0 (contrast zero time)\nDecimals instead of fractions with measurements: 0.5 volume (not one-half volume)\nBases use numerals (even those fewer than 10): 5 bases\nProbability\nUse an italic P or p. Use spaces around math symbols.\nSee also Statistics.\nProofreaders' Marks\nSome of you wonder about the shorthand-looking marks made on hard copies of your Web pages. This is a way of showing corrections and changes. There are just a few marks to learn, and they come in handy!\nHere is a nice link to view the marks: Proofreaders' Marks.\nPunctuation\nSee CBE, pp. 36-71.\nSee also Colons, Commas, Dashes, Hyphens, Quotation Marks, and Semicolons.\nQuotation Marks\nPlace quotation marks inside of punctuation.\nUse double quote marks. For quote marks inside of quote marks, use single quotes on the inside of the phrase and double quote marks on the outside of the phrase.\n\nExample:\n\nThe NCBI Handbook addresses PubMed's handling of Stopwords, specifically that \u201cPubMed ignores Stopwords, such as \u2018about\u2019, \u2018of\u2019, or \u2018what\u2019...\u201d, when processing simple searches.\nUse double quotation marks around phrases that some of the words begin with lowercase.\n\nExample:\n\nYou may also want to display your citations using \u201cSend to Text\u201d to eliminate the sidebar menu and toolbars before printing your results.\nIn the example above, the \u201cSend to Text\u201d phrase would not need quote marks if it were a hotlink because of the way links show up on the Web pages. The blue font would be enough to make it distinctive.\nAlso use double quotation marks to avoid confusion, as well as to show that you are implying a meaning somewhat different than that usually assumed (or that you doubt the validity of the usual meaning).\nRestriction Enzymes\nDo not use italics for the first three letters and close up the entire name, e.g., AccI, HaeII. Removal of italics is a change made by IUPAC in 2003.\nHelpful Tip\nVisit The Restriction Enzyme Database (REBASE). Select \u201cEnzyme Navigation Tables\u201d and \u201cAll enzyme names...\u201d for a complete list of restriction enzymes.\nSemicolons\nSee CBE, pp. 46-48, for the four general uses and five specialized uses of semicolons. Here are examples of common uses:\n\nExample:\n\nCertain treatments were more effective than others in eliminating the contaminating DNA; however, to achieve this there was a decrease in sensitivity.\n\nExample:\n\nLinks are provided to related Web sites including: chromosome databases (e.g., the Mitelman database); other NCI (e.g., CGAP and CCAP) and NCBI (e.g., the Map Viewer (Chapter 20) and LocusLink (Chapter 19) resources and PubMed (Chapter 2)) sites; The Jackson Laboratory; and several other CGH sites.\nSpelling\nAmerican spellings are preferred over British spellings.\nDifferences in spellings, from British to American, usually involve:\n\nswap of the letters \u201cr\u201d and \u201ce\u201d, such as \u201ccentre\u201d (British) and \u201ccenter\u201d (American)addition of the letter \u201cl\u201d, such as \u201ccancelled\u201d (British) and \u201ccanceled\u201d (American)use of letter \u201cs\u201d instead of letter \u201cz\u201d, such as \u201ccharacterise\u201d/\u201canalyse\u201d (British) and \u201ccharacterize\u201d/\u201canalyze\u201d (American)addition of letter \u201ca\u201d or \u201co\u201d with letter \u201ce\u201d, such as \u201chaematology\u201d/\u201cfoetus\u201d (British) and \u201chematology\u201d/\u201cfetus\u201d (American)addition of letter \u201cu\u201d, such as \u201ctumour\u201d/\u201cmould\u201d (British) and \u201ctumor\u201d/\u201cmold\u201d (American)use of \u201cph\u201d for \u201cf\u201d, such as \u201csulphate\u201d (British) and \u201csulfate\u201d (American)\n\nswap of the letters \u201cr\u201d and \u201ce\u201d, such as \u201ccentre\u201d (British) and \u201ccenter\u201d (American)\naddition of the letter \u201cl\u201d, such as \u201ccancelled\u201d (British) and \u201ccanceled\u201d (American)\nuse of letter \u201cs\u201d instead of letter \u201cz\u201d, such as \u201ccharacterise\u201d/\u201canalyse\u201d (British) and \u201ccharacterize\u201d/\u201canalyze\u201d (American)\naddition of letter \u201ca\u201d or \u201co\u201d with letter \u201ce\u201d, such as \u201chaematology\u201d/\u201cfoetus\u201d (British) and \u201chematology\u201d/\u201cfetus\u201d (American)\naddition of letter \u201cu\u201d, such as \u201ctumour\u201d/\u201cmould\u201d (British) and \u201ctumor\u201d/\u201cmold\u201d (American)\nuse of \u201cph\u201d for \u201cf\u201d, such as \u201csulphate\u201d (British) and \u201csulfate\u201d (American)\n1 gives a few examples of British and American spellings.\nBritish and American spellings\n|    | British       | American     |\n|---:|:--------------|:-------------|\n|  0 | analyse       | analyze      |\n|  1 | artefacts     | artifacts    |\n|  2 | cancelled     | canceled     |\n|  3 | centre        | center       |\n|  4 | characterise  | characterize |\n|  5 | colour        | color        |\n|  6 | criticise     | criticize    |\n|  7 | defence       | defense      |\n|  8 | emphasise     | emphasize    |\n|  9 | encyclopaedia | encyclopedia |\n| 10 | favour        | favor        |\n| 11 | foetus        | fetus        |\n| 12 | fulfill       | fulfil       |\n| 13 | grey          | gray         |\n| 14 | haematology   | hematology   |\n| 15 | immortalise   | immortalize  |\n| 16 | judgement     | judgment     |\n| 17 | licence       | license      |\n| 18 | mould         | mold         |\n| 19 | neighbour     | neighbor     |\n| 20 | organisation  | organization |\n| 21 | oxidise       | oxidize      |\n| 22 | prioritise    | prioritize   |\n| 23 | realise       | realize      |\n| 24 | recognise     | recognize    |\n| 25 | specialise    | specialize   |\n| 26 | stylised      | stylized     |\n| 27 | sulphate      | sulfate      |\n| 28 | summarise     | summarize    |\n| 29 | symbolise     | symbolize    |\n| 30 | tumour        | tumor        |\nInteresting Fact\nPubMed \u201ctranslates\u201d users' queries with British spellings into American spellings behind the scenes. For more information, read the NLM Technical Bulletin.\nStatistics\nIn general, variables are italicized, such as P for probability test, t test, U test; R for regression coefficient, r for correlation coefficient; n for total number.\nDistributions could be:\n\nexponential (duration)geometric (time to first success)Poisson (counting, rare events)normal (measurement error, asymptotic, approximations)uniformBernoulli (coin toss)binomial (sum of coin tosses)\n\nexponential (duration)\ngeometric (time to first success)\nPoisson (counting, rare events)\nnormal (measurement error, asymptotic, approximations)\nuniform\nBernoulli (coin toss)\nbinomial (sum of coin tosses)\nSome common variables used in bioinformatics are: CR (critical region); D (divergence); E (E-value), err (average training error); Err (true test error); F (distribution function); g; H (entropy); I (mutual information); K, k; P, p (probability); S (sample space); T, t; V (variance); X, x; Y, y; z.\n\nCommon terms are:\n\n--aggregating, model averaging\n--bagging, bootstrap aggregating\n--Bayes theorem\n--best-case scenario\n--BIC, Bayesian information criterion\n--bootstrap, replicate learning sets\n--Central limit theorem\n--Chebyshev's inequality\n--CI, confidence interval\n--COV, covariance\n--CV, coefficient of variance\n--cross-validation\n--eigen value\n--FDA, flexible discriminant analysis\n--Gaussian\n--Gini index\n--GLM, generalized linear model\n--Hessian\n--hyperplane\n--K-fold cross-validation\n--kernel functions\n--kNN, k nearest neighbor\n--IRLS, iterated reweighted least squares\n--Kolmogorov\u2013Smirnov\n--Lagrangian multipliers\n--Laplace approximation\n--LDA, linear discriminant analysis\n--least squares\n--LLR, likelihood ratio\n--logodds\n--Mahalanobis distance\n--MAR, missing at random\n--MCAR, missing completely at random\n--Markov chains\n--MDL, minimum description length\n--MLE, maximum likelihood error\n--model-fitted values\n--MoM, method of moments\n--MSE, mean square error\n--Newton\u2013Rhapson\n--Neyman\u2013Pearson\n--nonlinear\n--QQ-plots\n--PDA, penalized discrimnant analysis\n--SD, standard deviation\n--SE, standard error of the mean\n--Softmax, dummy regression\n--SRS, simple random sample\n--WLLN, weak law of large numbers\n--z-score\nSymbols\nAn abbreviated list of quantities, units, and symbols used in physical chemistry and related disciplines is available from IUPAC.\nSee pp. 815-818 in the CBE Index for a list of symbols.\nCBE provides the correct symbol representations for many diverse fields of science.\nIn Chapter 15 (Subatomic Particles, Chemical Elements, and Related Notations, pp. 251-259), you learn that IUPAC recommends roman letters for particle symbols, but the Particle Data Group uses italics for the elementary particles. By IUPAC standards, \u201ce\u201d stands for \u201celectron\u201d, and \u201ce stands for \u201celementary charge\u201d. The Particle Data Group uses e to mean \u201celectron\u201d.\n\nChapter 16 (Chemical Names and Formulas, pp. 260-304), p. 292, describes \u201cProtein Designations Based on Gene Names\u201d.\n\nExample:\n\n\u201cNames for proteins representing a mutant that is characterized by replacement of a single amino acid are sometimes derived from the corresponding gene symbol. For example, an amino acid replacement with valine at position 12 of the Ras protein may be indicated by RasVal12.\u201d (from CBE, p. 292)\nMore specific information on genes in particular can be found in Chapter 20 (Cells, Chromosomes, and Genes) on pp. 334-380. In general, genes are shown in italics and proteins are shown as roman, but when listing many, many genes, it is not helpful to use this style. You must use your judgment when deciding on when to show genes in an italic style.\n\nViruses are covered in Chapter 21 (pp. 381-394), Bacteria in Chapter 22 (pp. 395-410), Plants, Fungi, Lichens, and Algae in Chapter 23 (pp. 411-445), and Human and Animal Life in Chapter 24 (pp. 446-485). Within Chapter 24 is a detailed description of taxonomy.\nThere are other interesting chapters in the \u201cSpecial Scientific Conventions\u201d section of CBE as well.\nTime\nConvert military time (0600\u20131800) to AM/PM time (6 a.m.\u20136 p.m.; 6:30 a.m.\u20136:30 p.m.). Include time zone and daylight/standard time designations, if necessary.\nUnits of time: year, month, week, day, hour, min, sec. Only \u201cmin\u201d and \u201csec\u201d are abbreviated.\nTrademarks, Trade/Supplier Names\nUse superscript TM or \u00ae when known, at first occurrence only.\nAt first mention of a company name, use its full form (e.g., Sigma Chemical Co.).\nIt is OK to abbreviate Co., Inc., Ltd., etc. Thereafter, refer to the company with a shortened version (e.g., Sigma). No need to supply city/state information. If items have been provided as gifts, provide city/state information (no postal code).\nUnits of Measure\nSee the CBE Index of \u201csymbols(s)\u201d, beginning on page 815.\nUse \u201cml\u201d for milliliter, \u201cmol\u201d for mole, and \u201cM\u201d for mol/l. \u201cLiter\u201d is written out when used alone.\n\nversus\nUse italics.\nWrite out \u201cversus\u201d in text, but it is OK to use \u201cvs.\u201d in tables.\nX-ray\nUse a capital X wherever the term appears.", "pairs": [], "interleaved": []}
 {"file": "styleguide_NBK988/A380.nxml", "text": "It is not possible to remember all of the standards set by official bodies, but yet you must follow the rules and be consistent. You can turn to these guides for help.\nWe use the following resources as standards and guides to style.\n\nFor overall guidance, use:\n\n\nCouncil of Biology Editors. Scientific style and format. 6th ed. Cambridge (UK): Cambridge University Press; 1994.\n\nCouncil of Biology Editors. Scientific style and format. 6th ed. Cambridge (UK): Cambridge University Press; 1994.\nThis book is good because it covers many scientific disciplines in detail and references the decisions of important international committees. The 7th edition will be available June 2006. You can preview some of the changes.)\n\nFor questions of reference style, use:\n\n\nPatrias K. National Library of Medicine recommended formats for bibliographic citation. Bethesda (MD): U.S. Department of Health and Human Services, Public Health Service, National Institutes of Health; 1991.Patrias K. National Library of Medicine recommended formats for bibliographic citation. Supplement: internet formats. Bethesda (MD): U.S. Department of Health and Human Services, Public Health Service, National Institutes of Health; 2001.\n\n\nPatrias K. National Library of Medicine recommended formats for bibliographic citation. Bethesda (MD): U.S. Department of Health and Human Services, Public Health Service, National Institutes of Health; 1991.\nPatrias K. National Library of Medicine recommended formats for bibliographic citation. Supplement: internet formats. Bethesda (MD): U.S. Department of Health and Human Services, Public Health Service, National Institutes of Health; 2001.\n\nThis pair of documents is probably the most complete recording of reference requirements you\nmay ever see. PDFs for these documents are available. By\nthe end of 2006, an updated, combined electronic version will be available on the Bookshelf as\n\u201cCiting Medicine: The NLM Style Guide for Authors, Editors, and Publishers\u201d.\nFor a\nquick overview of reference styles in \u201cThe NCBI Style Guide\u201d, see Special Content, References.\n\nFor questions of chemical style, use:\n\n\n International Union of Pure and Applied Chemistry and International Union of Biochemistry and Molecular Biology. IUPAC-IUBMB Joint Commission on Biochemical Nomenclature and Nomenclature Commission of IUBMB. Available from: IUPAC.\n\n\n International Union of Pure and Applied Chemistry and International Union of Biochemistry and Molecular Biology. IUPAC-IUBMB Joint Commission on Biochemical Nomenclature and Nomenclature Commission of IUBMB. Available from: IUPAC.\n\nThis Union is the nomenclature authority.", "pairs": [], "interleaved": []}
 {"file": "styleguide_NBK988/A135.nxml", "text": "Before beginning any writing project, review the guidelines for plain language. These guidelines will provide the foundation for your writing project.\nBegin your writing project with a short list of topics to cover; more ideas will come to you once you've taken this small step.\nThe brief pointers in the bulleted list will help you now and later.\n\n Prepare your materials for presentation to an international audience. Use common words, where possible, but be precise. Use a combination of active and passive voice. Present text, tables, graphics, and other materials clearly, concisely, and consistently. For the Web environment in particular, divide your thoughts into manageable sections.\n\n Prepare your materials for presentation to an international audience.\n Use common words, where possible, but be precise.\n Use a combination of active and passive voice.\n Present text, tables, graphics, and other materials clearly, concisely, and consistently.\n For the Web environment in particular, divide your thoughts into manageable sections.", "pairs": [], "interleaved": []}
 {"file": "styleguide_NBK988/A201.nxml", "text": "This chapter contains basic information, such as \u201cSubject-Verb Agreement\u201d, as well as more unusual aspects of writing, such as \u201cAnthropomorphism\u201d.\nAnthropomorphism\n\nAnthropomorphism is \u201can interpretation of what is not human or personal in terms of human or personal characteristics\u201d (Merriam-Webster's Collegiate Dictionary. Tenth Edition. Springfield (MA): Merriam-Webster, Inc.; 2002). You can read more about it in the Merriam-Webster Online Dictionary.\nAnthropomorphism seems to occur more frequently in texts about software.\n\nExample:\n\nA function to determine all features in a particular region of a Bioseq need not care what types of features they are.\n\nRewrite as:\n\nA function to determine all features in a particular region of a Bioseq is not affected by what types of features there are.\nAlthough text that has been anthropomorphosized may be entertaining, an international audience is better served by presenting text in a straightforward manner.\nCommon Errors\nHere are the top seven errors, with specific examples of correct usage underlined.\n\n\u201cas/because\u201d\n\nDo not use \u201cas\u201d when \u201cbecause\u201d is meant.\nSupplied as: The polyA tail of an mRNA (cDNA) sequence should never be trimmed as it provides a useful landmark.\nShould be: The polyA tail of an mRNA (cDNA) sequence should never be trimmed because it provides a useful landmark.\n\n\u201ccomprise\u201d and \u201ccompose\u201d\n\nRemember that \u201cthe whole comprises the parts\u201d. The following examples use the words correctly.\nThe FMR1 gene comprises 18 exons interspersed over ~40,000 base pairs of sequence.\nThe Alu repeat family comprises short, interspersed elements present in multiple copies in the genomes of humans and other primates.\nThe second model comprises three closely spaced exons.\nOMIM comprises descriptive, full-text MIM entries, a tabular synopsis of the Human Gene Map, clinical synopses, and mini-MIMs.\nSegmented Bioseqs are composed of pointers to other raw sequences in GenBank.\nNever use \u201ccomprised of\u201d. Use \u201ccomposed of\u201d instead.\n\n\u201cdue to\u201d\n\nDo not use \u201cdue to\u201d as a substitute for \u201cbecause of\u201d or \u201cattributable to\u201d. These sentences are correct.\n\u2026or whether the similarity observed is attributable to chance alone.\nMuch of the success of the project is attributable to the flood of new molecular data.\nThe term refers to similarity attributable to descent from a common ancestor.\nMany of them exist in the coding region of a gene, but the precise location cannot be resolved because of an error in the alignment of the exon.\nIf a gene has multiple transcripts because of alternative splicing, then a variation can have several different functional relationships to the gene.\nGenBank annotation staff would respond to a request for a list of Accession numbers that are due to appear in upcoming issues of a publisher\u2019s journal(s).\n\n\u201cfrom\u2026 to \u2026\u201d and \u201cbetween\u2026 and \u2026\u201d\n\nThe \u201cfrom\u2026 to \u2026\u201d construction contains the end points, but the \u201cbetween\u2026 and \u2026\u201d construction excludes the end points.\nNo space is allowed between the value and the field name.\nFMR1 resides somewhere between markers DXS532 and DXS7389.\nThe bars represent matches from residues 3 to 60.\n\n\u201cit's\u201dversus\u201cits\u201d\n\n\u201cIt's\u201d is a contraction of \u201cit is\u201d. If you are having trouble using \u201cit's\u201d, just substitute \u201cit is\u201d in your sentence and see if it makes sense. If so, then you are using \u201cit's\u201d correctly. \u201cIts\u201d, on the other hand, shows possession or refers to itself. Most errors occur because of the incorrect use of the contraction\u2014\u201cit's\u201d. The confusion probably arises from the way in which possessives are formed in English, for example, Belinda's cat, Jeff's boat, but its mechanism, etc.\nThe sequence of each exon is an individual raw Bioseq in its own right.\n\nIt's the lock that is lost, not its combination.\n\n\u201csince/because\u201d\n\nUse \u201csince\u201d when referring to time.\nDuring each build, we cluster the data submitted since the last build into the existing refSNPs and form new refSNPs when necessary.\nThe set of new data entering each build typically includes all submissions received since the close of data in the previous build.\nData are presented by quarter since operations began on July 25, 2000.\n\nBecause the execution of the search algorithm is decoupled from the formatting, the results can be delivered in a variety of formats without rerunning the search.\nXML is also structured output but can be produced from ASN.1 because it has equivalent information.\n\n\u201cwhich/that\u201d\n\nThe word \u201cwhich\u201d usually introduces information that is \u201cextra\u201d (or interesting but not the point being made at the time), meaning that the sentence is complete and imparts what is necessary without the information that is introduced by \u201cwhich\u201d. The word \u201cthat\u201d, on the other hand, introduces information that is necessary to understanding the meaning/intent of the sentence.\nThe resulting file, which PHRAP outputs in \u201c.ace\u201d format, consists of the sequence itself plus the associated quality scores.\nThe alignment information is extracted into a Seq-align, which is packaged as annotation (Seq-annot) associated with the BioSeqSet.\nAn Entrez \u201cnode\u201d is a collection of data that is grouped together and indexed together.\nEntrez is designed to infer relationships between different data that may suggest future experiments or assist in interpretation of the available information.\nGender Neutral\nUse gender-neutral language.\nFor example, change:\nmankind \u2192 humanity\nbest man for the job \u2192 best person for the job\nthe common man \u2192 average person, ordinary people\nmailman \u2192 mail carrier\ncongressman \u2192 congressional representative\npoliceman \u2192 police officer\nOther ways to handle this problem are to recast a sentence in the plural, reword to eliminate gender problems, or replace the masculine pronoun with \u201cone\u201d or \u201cyou\u201d.\nHedging\nHedging takes place when an author wants to \u201cevade the risk of commitment especially by leaving open a way of retreat\u201d (Merriam-Webster's Collegiate Dictionary. Tenth Edition. Springfield (MA): Merriam-Webster, Inc. 2002). Usually, the sentence will read something like, \u201cThis assay may provide a better way of identifying mutant genes\u201d. It is reasonable to temper one's confidence about a new method.\nSometimes authors do not realize they are using a kind of hedging when they unintentionally express a lack of confidence by using certain phrases, such as \u201cintends to\u201d, \u201caims to\u201d, and \u201chas the goal of\u201d.\nExamine this sentence: \u201cGenBank aims to provide a searchable database of sequences.\u201d\nContrast that sentence with this one: \u201cGenBank is a searchable sequence database\u201d.\nThis is a more confident statement, and the reader is not distracted from the main thought.\nPoint of View: First Person, Second Person, Third Person\nThe point of view describes whether a person is:\n\n\ndescribing events as a participant, such as \u201cI raced to catch the train before it could enter the tunnel\u201d (told in the first person because it uses \u201cI\u201d)\ngiving instructions to someone directly, such as \u201cYou must catch the train before it reaches the tunnel\u201d (\u201cyou\u201d is used for second person)\nrelating events about others, such as \u201cHe failed to catch the train before it reached the tunnel\u201d (third person because of \u201che\u201d)\n\n\ndescribing events as a participant, such as \u201cI raced to catch the train before it could enter the tunnel\u201d (told in the first person because it uses \u201cI\u201d)\n\ngiving instructions to someone directly, such as \u201cYou must catch the train before it reaches the tunnel\u201d (\u201cyou\u201d is used for second person)\n\nrelating events about others, such as \u201cHe failed to catch the train before it reached the tunnel\u201d (third person because of \u201che\u201d)\nThe most common error occurs when different points of view are mixed; usually, the second-person \u201cyou\u201d is mixed with a third person point of view:\n\nExample:\n\n\u201cThe data are entered as field names. One must be careful to end each field name with a delimiter code. You don't have to worry about whether the delimiter code is in uppercase or lowercase. One must then exit this subroutine to run the next portion of the program.\u201d\nIn the example above, the second-person \u201cyou\u201d has been used in a paragraph of third-person sentences. To keep the same point of view, one could have said, \u201cOne does not have to worry about whether the delimiter code is in uppercase or lowercase.\u201d\nSometimes \"one\" is considered a little formal. If a formal approach is not needed, consider this approach, which uses an implied \"you\":\n\u201cEnter the data as field names, being careful to end each field name with a delimiter code. Either uppercase or lowercase may be used in delimiter codes because they are case insensitive. After entering all of the data, exit the subroutine and continue with the next programmed task.\u201d\nFirst person uses: I, we\n\nSecond person uses: you\n\nThird person uses: he, she, it, one, they\n\nCheck your text for consistency in the use of point of view. Check the use of \u201cyou\u201d first.\nScientific English: Past, Present, and Simple\nOne of the finer points of science writing in English is the expression of the degree of acceptance of information by the use of present tense and past tense. Established knowledge (statements of fact, natural laws, universal (established) truths, or a widely held tenet of science) is given in the simple present tense, and the new results and findings of an author's own research are given in the simple past tense. Once an author's findings are published and become an established truth (generally accepted by experts in the field), they are referred to in the present tense.\nThese ideas are complex but are illustrated below:\nSimple present tense:\n--PubMed Central is the National Library of Medicine\u2019s digital archive of full-text journal literature.\n--Entrez is the text-based search and retrieval system used at NCBI for all of the major databases.\nSimple past tense (isolates the event in the past):\n--The cells were produced by continuous proliferation of the hybridoma cell line.\n--The lytic ability of the T8 cell subset was examined.\nSome authors, especially those whose native language is not English, are not as aware that the use of past and present tenses signals the status of the presented information. Because the use of the simple present tense signals that something is a general truth, the reader is given some feeling of certainty about the information. A misinterpretation of the significance of the findings could occur if the wrong tense is used. The use of the simple present tense when first presenting one\u2019s own findings could be perceived as arrogant as well.\nEven the demonstration of significant results in one's own study is not a reason for using the present tense in the Discussion section of the paper first reporting those results. However, explanations of graphical presentations of data, such as tables and figures, should use the present tense. For example, when referring to3, it is fine to say: \u201c3 shows that the mean yield is lower than expected.\u201d.\n\nNote to Authors: To avoid misunderstanding, report your findings in the past tense.\nA fascinating, detailed account of this convention is provided in:\n\nBurrough-Boenisch J. Examining present tense conventions in scientific writing in the light of reader reactions to three Dutch-authored discussions. English for Specific Purposes 2003;22(1):5-24.\n\nBurrough-Boenisch J. Examining present tense conventions in scientific writing in the light of reader reactions to three Dutch-authored discussions. English for Specific Purposes 2003;22(1):5-24.\nAdditional information about the use of tenses in science is provided in:\n\nMatthews JR, Bowen JM, Matthews RW. Successful scientific writing: a step-by-step guide for biomedical scientists. 2nd edition. Cambridge: Cambridge University Press; 2001.\n\nMatthews JR, Bowen JM, Matthews RW. Successful scientific writing: a step-by-step guide for biomedical scientists. 2nd edition. Cambridge: Cambridge University Press; 2001.\n\nAcknowledgment: My sincere thanks go to Joy Burrough-Boenisch for reviewing this section on \u201cScientific English: Past, Present, and Simple\u201d. Any errors that remain are entirely my own.---Belinda Beck\nSubject\u2013Verb Agreement\nSubject and verb agreement means that if the subject is singular, the verb must be singular. If the subject is plural, the verb must be plural. This sounds very simple, but people run into trouble because of intervening phrases (phrases that come between the subject and the verb). For example, this type of sentence gives many people trouble:\n\n The number of birds was impressive.\n\n The number of birds was impressive.\nThe subject of the sentence is \u201cnumber\u201d (singular), and the verb is \u201cwas\u201d (singular). The plural word \u201cbirds\u201d is part of a prepositional phrase (that intervenes between the subject and the verb) and therefore is not considered when checking for subject\u2013verb agreement.\nVoice: Active versus Passive\nWhen the subject of the sentence performs the action of the verb, the sentence has been constructed in active voice.\n\nI hit the ball across the yard.\n\nI hit the ball across the yard.\nIf the subject is being acted upon, then the sentence has been constructed in the passive voice.\n\nThe ball was hit across the yard.\n\nThe ball was hit across the yard.\nThe choice of active or passive sentence structure affects the emphasis in the sentence (see also \u201cEmphasis\u201d in the section Style Points and Conventions). The beginning of the sentence receives more emphasis in the active voice. The end of the sentence receives more emphasis in the passive voice. Both can be used to advantage.\nPassive Voice\n\nAdvantages of passive voice:\n\n\nminimizes or leaves out the role of the person performing an action (for cases where you do not know who did it, do not want to mention who did it, or who did it is irrelevant)softens the tone or makes the message less personal\n\nminimizes or leaves out the role of the person performing an action (for cases where you do not know who did it, do not want to mention who did it, or who did it is irrelevant)\nsoftens the tone or makes the message less personal\n\nDisadvantages of passive voice:\n\n\nmakes the sentence wordy and awkwardadds formality\n\nmakes the sentence wordy and awkward\nadds formality\nSentences constructed in passive voice often begin with \u201cThere is\u201d and \u201cThere are\u201d. Most sentences can be improved by changing to active voice:\n\n\nInstead of: \u201cThere are dozens of research resources at NCBI.\u201d\nConsider: \u201cNCBI offers dozens of research resources.\u201d\n\n\nInstead of: \u201cThere are dozens of research resources at NCBI.\u201d\n\nConsider: \u201cNCBI offers dozens of research resources.\u201d\nActive Voice\n\nAdvantages of active voice:\n\n\nShorter sentences are easier to read (\u201cwas\u201d and \u201cby\u201d are usually eliminated).Sentences are more dynamic, forceful, clearer, stronger, and concise.\n\nShorter sentences are easier to read (\u201cwas\u201d and \u201cby\u201d are usually eliminated).\nSentences are more dynamic, forceful, clearer, stronger, and concise.\n\nDisadvantage of active voice:\n\n\nSentence overuse emphasizes the doer of the action.\n\nSentence overuse emphasizes the doer of the action.\nMixing Voices\nDo not mix active and passive constructions in the same sentence. An easy way to check for passive voice is by asking, \u201cWho did that?\u201d If you cannot give a definite answer, the sentence is passive.\nScientific writing most often uses passive sentence construction to give the author less importance and to focus attention on the facts at hand. But scientific writing can be made more engaging by using some sentences in active voice as well.\nStrike a balance between the use of active voice and passive voice. Both have their uses. Consider the emphasis in the sentence and whether the sentence needs to be more dynamic. The use of more constructions in the active voice makes text more engaging.\nWordy Constructions to Avoid, Substitutions of Common Phrases, Plainer Synonyms\nTo write concisely, you must eliminate superfluous detail. Sometimes, this is just a matter of eliminating some phrases altogether. Take the phrase \u201cis designed to\u201d. Unless the design is the point of the sentence, drop this phrase. Type this search in Google: \u201cis designed to\u201d site:ncbi.nlm.nih.gov. Look at the results and try mentally dropping the phrase \u201cis designed to\u201d. Was the sentence adversely affected or improved?\nThe following list contains helpful suggestions for writing more succinctly.\na number of \u2192 few, many, several, some\na majority of \u2192 most\naccordingly \u2192 therefore\naccounted for the fact that \u2192 because\nactually \u2192 (consider eliminating this word)\nadditional \u2192 more, added, other\nadditionally \u2192 and, also\nadequate number of \u2192 enough\nadjacent to \u2192 close to, near, next to\nadvantageous \u2192 useful, helpful\nalong the lines of \u2192 similar to\nan innumerable number of \u2192 innumerable, countless, many\nan order of magnitude \u2192 10 times\nantecedent to \u2192 before\nanterior to \u2192 before\nanticipate \u2192 expect\nany particular type of \u2192 any\nare of the same opinion \u2192 agree\nas a consequence of \u2192 because of\nas a means to \u2192 to\nas a result of \u2192 because of, from\nas far as our own observations are concerned, they show \u2192 we observed\nas regards \u2192 about, concerning\nas to \u2192 on, for, about, of\nascertain the location of \u2192 find\nat an early date \u2192 soon\nat present \u2192 now, currently\nat such time as \u2192 when\nat the place where \u2192 where\nat the present moment \u2192 now\nat the present time \u2192 now\nat the time that \u2192 when\nat this point in time \u2192 now\nbasically \u2192 (consider eliminating this word)\nbecause of the fact that \u2192 given that\nby means of \u2192 with, in, by\nby reason of \u2192 because of\nby virtue of \u2192 by, under, because of\ncaused injuries to \u2192 injured\ncompletely filled \u2192 filled\nconcerning the matter of \u2192 on, for\nconcur \u2192 agree\nconnect together \u2192 by\nconsequence \u2192 result\nconsequently \u2192 therefore\nconsider all factors carefully \u2192 consider\nconsolidate \u2192 combine, join\nconstitute \u2192 make up\ndeem \u2192 consider, think, treat as\ndefinitely \u2192 (consider eliminating this word)\ndefinitely proved \u2192 proved\ndemonstrate \u2192 show, prove\ndesignate \u2192 appoint, name, choose, set\ndespite the fact that \u2192 although\ndiminish \u2192 lessen, reduce\ndiscontinue \u2192 stop\ndue to the fact that \u2192 because\nduring such time as \u2192 while\nduring the course of \u2192 during, while\nduring the period from \u2192 from\nduring the time that \u2192 while, when\nelucidate \u2192 explain, clarify\nenumerate \u2192 list, name\nequally as \u2192 equally\nequivalent \u2192 equal, the same\nexcessive number of \u2192 too many\nfabricate \u2192 build, make\nfacilitate \u2192 make easier, help\nfewer in number \u2192 fewer\nfollowing \u2192 after\nfor a period of \u2192 for\nfor all intents and purposes \u2192 (consider eliminating this phrase)\nfor the purpose of \u2192 to, for\nfor the purpose of examining \u2192 to examine\nfor the reason that \u2192 because\nfrequently \u2192 often\nfrom the point of view of \u2192 from, for\nfurthermore it would seem \u2192 and\ngenerally \u2192 (consider eliminating this word)\ngive proper consideration to \u2192 consider\ngive rise to \u2192 cause\ngoes under the name of \u2192 is called\nfuture plans \u2192 plans\nhas a tendency to \u2192 tends\nhas the ability to \u2192 can\nhas the capability of \u2192 can, is able\nhas discretion to \u2192 may\nhave a negative impact \u2192 hurt, harm\nhence \u2192 therefore\nidentical \u2192 same\nif conditions are such that \u2192 if, when\nillustrate \u2192 show\nimpact \u2192 affect, influence\nimplement \u2192 carry out, begin, start, create, set up\nin a precise manner \u2192 precisely\nin a satisfactory manner \u2192 satisfactorily\nin a situation where \u2192 if, when\nin addition to \u2192 besides, also\nin all cases \u2192 always, invariably\nin an adequate manner \u2192 adequately\nin back of \u2192 behind\nin case \u2192 if\nin close proximity to \u2192 near\nin connection with \u2192 with, about, concerning, for\nin excess of \u2192 more than, over\nin favor of \u2192 for\nin lieu of \u2192 instead of, rather than\nin order to \u2192 to, for\nin proximity to \u2192 close to, near\nin reference to \u2192 on, for\nin regard to \u2192 on, for\nin relation to \u2192 on, for\nin spite of the fact that \u2192 although\nin terms of \u2192 in, for, about\nin the absence of \u2192 without\nin the amount of \u2192 for\nin the case in which \u2192 when\nin the case of \u2192 in, with\nin the course of \u2192 during, while\nin the event that \u2192 if, when\nin the nature of \u2192 like, similar to\nin the near future \u2192 soon\nin the neighborhood of \u2192 about, roughly\nin the place in which \u2192 where\nin this instance, however \u2192 but\nin view of the fact that \u2192 because\nin the vicinity of \u2192 close to, near\ninasmuch as \u2192 given that\ninception \u2192 start, beginning\nindicate \u2192 show, suggest\nindication \u2192 sign\nindividual \u2192 person\ninitial \u2192 first\ninitiate \u2192 begin, start, set up\ninstitute \u2192 begin, start, set up\nis able to \u2192 can\nis authorized to \u2192 may\nis capable of \u2192 can\nis in a position to \u2192 can, may\nis permitted to \u2192 may\nit has been reported by Smith \u2192 Smith reported\nit is (omit)\nit is believed that (omit)\nit is felt that (omit)\nit is important that \u2192 must, should\nit is necessary that \u2192 must, should\nit is often the case that \u2192 often\nit is possible that the cause is \u2192 the cause may be\nit is probable that \u2192 probably\nit is this that \u2192 this\nit is worth pointing out that \u2192 note that\nit would appear that \u2192 apparently\nit would thus appear that \u2192 apparently\nkind of \u2192 rather (or consider eliminating this phrase)\nlacked the ability to \u2192 could not\nlarge amounts of \u2192 much\nlarge in size \u2192 large\nlarge numbers of \u2192 many\nlocated in \u2192 in\nlocated near \u2192 near\nmagnitude \u2192 size\nmanufacture \u2192 make\nmethodologies \u2192 methods\nmodification \u2192 change\nmodify \u2192 change\nnecessitate \u2192 require\nnecessitates the inclusion of \u2192 needs, requires\nnecessity \u2192 need, requirement\nno later than September 30 \u2192 before October 1\nnotification \u2192 notice\nnotwithstanding \u2192 despite\nnotwithstanding the fact that \u2192 although\nnumerous \u2192 many\nobjective \u2192 goal, aim\non a daily basis \u2192 daily, every day\non account of \u2192 because\non behalf of \u2192 for\non or before September 30 \u2192 before October 1\non the basis of \u2192 by, from, because of\non the grounds that \u2192 because\non the part of \u2192 by\non the occasion of \u2192 on\non the part of \u2192 by\nongoing \u2192 continuing, active\nopt for \u2192 choose\noptimum \u2192 best\noption \u2192 choice\noval in shape, oval-shaped \u2192 oval\nowing to the fact that \u2192 because\nparameter \u2192 limit, boundary, guideline, condition\nparticular \u2192 (consider eliminating this word)\npast history \u2192 history\npreclude \u2192 prevent\npreferable \u2192 best, better, preferred\nposterior to \u2192 after\nprevious \u2192 earlier, last, past\nprevious to \u2192 before\npreviously \u2192 before, earlier\nprincipal \u2192 main, chief\nprior \u2192 earlier\nprior to \u2192 before\nprovided that \u2192 if, but\nreally \u2192 (consider eliminating this phrase)\nreferred to as \u2192 called\nregarding \u2192 about, on, for\nrepresents \u2192 is, makes up, stands for\nresponsible for \u2192 causes, has charge of\nresults so far achieved \u2192 results thus far, results to date\nretain \u2192 keep\nround in shape \u2192 round\nserves the function of being \u2192 is\nsituated \u2192 placed, sits, lies\nsmaller in size \u2192 smaller\nsort of \u2192 (consider eliminating this phrase)\nsubsequent to \u2192 later, after\nsubsequently \u2192 later, afterwards, then\nsufficient \u2192 enough\nsufficient number of \u2192 enough\ntake into consideration \u2192 consider\nterminate \u2192 end, stop\ntermination \u2192 end\nthe organism in question \u2192 this organism\nthe majority of \u2192 most\nthe question as to whether \u2192 whether\nthe reason why is that \u2192 because\nthe tests have not as yet \u2192 the tests have not\nthe treatment having been performed \u2192 after treatment\nthere are (omit)\nthere can be little doubt that this is \u2192 this probably is\nthere is (omit)\nthere is a need for \u2192 must, should\nthis is a subject that \u2192 this subject\nthis is a topic that \u2192 this topic\nthere is no doubt but that \u2192 doubtless, no doubt\nthrough the use of \u2192 by, with (not \u201cvia\u201d)\nthroughout the entire area \u2192 throughout the area\nthroughout the whole experiment \u2192 throughout the experiment\ntranspire \u2192 happen\ntype of \u2192 (consider eliminating this phrase)\ntwo equal halves \u2192 halves\nunder circumstances in which \u2192\nunder the provisions of \u2192 under\nuntil such time as \u2192 until\nused to fulfil \u2192 needed\nutilize \u2192 use\nvisualize \u2192 think of, imagine\nwarrant the use of \u2192 must or should have, require\nwas of the opinion that \u2192 believed\nwith a view to \u2192 to, for\nwith a view to getting \u2192 to get\nwith reference to \u2192 about\nwith regard to \u2192 about, concerning\nwith respect to \u2192 on, for\nwith the exception of \u2192 except for\nwith the object of \u2192 to, for\nwith the result that \u2192 so that\nwithout some kind of \u2192 without", "pairs": [], "interleaved": []}
-{"file": "styleguide_NBK988/A402.nxml", "text": "Appendices, Boxes, Figures, References, and Tables are listed as \u201cSpecial Content\u201d because they have more styling issues associated with them, and it is harder to make them consistent (but not impossible!).\nAppendices\nUse Arabic numbers when the there is more than one Appendix. Give a brief title, capitalizing the first word of the title and using lowercase thereafter. Capitalize the first word after a colon, unless it is a designation or abbreviation that is lowercase. Place a period after the title. Appendices appear after Acknowledgments and Addendums and before References.\n\nExample:\n\nAppendix 1. FASTA identifiers: Identification of sequence source databases.\nBoxes\nThis format sets information in a separate box from the text, accessible from the text by a link and from the jump list on the left of the screen (sidebar).\nNumber the boxes consecutively with Arabic numbers followed by a period. Capitalize the first word of the title and use lowercase thereafter. If the title contains a colon, the word after the colon is capitalized, unless that word is a designation or abbreviation that begins with a lowercase letter. This is the same title style as Tables.\n\nExample:\n\nBox 1. Approaches to associate sequence data with LocusLink loci.\nFigures\nWrite out the word \u201cFigure\u201d in the text and legends.\nIn legends, the title is written in bold on a separate line from the additional information. Italicize the locants and the parts of the figure. Locants may be in lowercase or uppercase, but be consistent.\nThe word \u201cpanel\u201d can usually be avoided. Be sure that all symbols on the figure are described. Refer to symbols as \u201cfilled\u201d (not \u201csolid\u201d) and to lines as \u201cunbroken\u201d (not \u201csolid\u201d).\n\nExample:\n\n----------------------------------------\n\nKaryotype parser.\n\nThe short-form written karyotype (a) has been converted into a modified long-form karyotype (b).\n----------------------------------------\nNote the position of the locants in the figure legend. The locant follows the information it describes. Locants given in a series format are styled: a, fresh samples; b, desiccated samples.\nWhen referring to the figure in the text, use roman-style locants (\u201c7a\u201d). When you want to refer to two parts of the figure (such as \u201c7, a and b\u201d) and the figure contains only two parts, change the text entry to read \u201c7\u201d. If the figure contains more than two parts and you are referring to two parts, show \u201c7, a and b\u201d.\nReferences\nCite references in the text in the proper order (numerically) as full-size, on-line numbers within parentheses. Number the references in the References section consecutively. References cited only in tables and figures are listed after those that have been cited in the text.\nReferences \u201cin press\u201d are cited in the References section of the paper. Unpublished work, manuscripts in preparation or submitted for publication, verbal reports given at meetings, and personal communications are cited in the text in parentheses (or as footnotes).\nUse of et al.: References in a paper that are linked with a PubMed ID or to the NCBI Bookshelf should still list all authors. In projects where space is an issue (such as in abut not in the References), it is acceptable to use one author with et al.\nUnlike titles in boxes, tables, and figures that use a capital in the first word after a colon, the part of the title in a reference after a colon is not capitalized (unless it is a proper noun, designation, or other form that takes a capital letter anyway).\nUse the NLM style for format. See the styles below for examples of this format. See also Sample PubMed Central Citations - XML Tagged and select the \u201cuntagged version\u201d from the page. For PDFs of the recommended formats, see Recommended Formats for Bibliographic Citation and Supplement: Internet Formats.\nBooks\nSingle author--\n1. Salton G. Automatic text processing. Reading (MA): Addison-Wesley; 1989.\nMore than one author\u2014\n2. Sankoff TF, Kruskal JB. Time warps, string edits and macromolecules: the theory and practice of sequence comparison. Reading (MA): Addison-Wesley; 1983.\nWith editors\u2014\n3. Altschul SF. Evaluating the statistical significance of multiple distinct local alignments. In: Suhai S, editor. Theoretical and computational methods in genome research. New York: Plenum Press; 1997. p. 1-14.\nChapter from a book\u2014\n4. Mizrachi I. GenBank: the nucleotide sequence database. In: McEntyre J, editor. The NCBI handbook [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2002 Oct. Available from: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books\nJournals\nSingle author\u2014\n1. Lipman DJ. Making (anti)sense of non-coding sequence conservation. Nucleic Acids Res 1997 Sep 15;25(18):3580-3583. Review.\nMore than one author\u2014\n2. Benson DA, Boguski MS, Lipman DJ, Ostell J. GenBank. Nucleic Acids Res 1997 Jan 1;25(1):1-6.\nInternet\n1. Patrias K. National Library of Medicine recommended formats for bibliographic citation. Supplement: internet formats [Internet]. Bethesda (MD): National Library of Medicine; 2001 Jul [cited 2001 Aug 8]. 106p. Available from: http://www.nlm.nih.gov/pubs/formats/internet.pdf\n\nTables\nThe word \u201cTable\u201d should be capitalized and spelled out, followed by an arabic number and a period. Give the table a brief title, followed by a period. If the title contains a colon, capitalize the word after the colon (unless it is a designation or abbreviation that is shown in lowercase). Additional descriptive material may be given in a paragraph below the title. Use superscript, lowercase, italic letters for footnote citations. Change abbreviations such as \u201cn.d.\u201d (\u201cnot done\u201d), \u201cn.s.\u201d (\u201cnot significant\u201d), and \u201cn.a.\u201d (\u201cnot applicable\u201d) to ND, NS, and NA, respectively.\n\nExample:\n\n1 ID system: ProductsTypeSourceASN.1GBFFa\nQscoreGenPeptProtein FASTACumulativeGenBankXXXXIncrementalGenBankXXXXIncrementalGenBankb\nXXCumulativeRefSeqXXXXIncrementalRefSeqXXXXa\nGBFF, GenBank flatfile.b\nNCBI records only.\n\n ID system: Products\n|    | Type        | Source   | ASN.1   | GBFFa   | Qscore   | GenPept   | Protein FASTA   |\n|---:|:------------|:---------|:--------|:--------|:---------|:----------|:----------------|\n|  0 | Cumulative  | GenBank  | X       | nan     | X        | X         | X               |\n|  1 | Incremental | GenBank  | X       | nan     | X        | X         | X               |\n|  2 | Incremental | GenBankb | nan     | X       | X        | nan       | nan             |\n|  3 | Cumulative  | RefSeq   | X       | X       | nan      | X         | X               |\n|  4 | Incremental | RefSeq   | X       | X       | nan      | X         | X               |\n\nGBFF, GenBank flatfile.\n\nNCBI records only.", "pairs": [], "interleaved": []}
 {"file": "styleguide_NBK988/A146.nxml", "text": "Our Web pages must communicate our ideas clearly and effectively, and the visual aspects are as important as the text. Navigation must be easy, and some thought must be given to the interaction experience of the user.\nGoing Public\nNCBI has an international audience. Because humor does not translate well into other languages, keep instructions clear and concise.\nAvoid jargon, slang, and nonstandard usages.\n\nDo not use \u201cflavors\u201d when you mean styles, formats, or varieties. Instead of writing \u201cGenBank submission tools come in three flavors\u201d, write \u201c NCBI provides three GenBank submission tools\u201d.Avoid using \u201callow\u201d to mean that computer resources or controls provide a service. Instead of writing \u201cMy NCBI allows users to store searches\u201d, write \u201cMy NCBI stores searches for users\u201d.Do not write that a computer \u201ccrunches\u201d data---\u201cprocesses\u201d, or a similar term, is more appropriate.\n\nDo not use \u201cflavors\u201d when you mean styles, formats, or varieties. Instead of writing \u201cGenBank submission tools come in three flavors\u201d, write \u201c NCBI provides three GenBank submission tools\u201d.\nAvoid using \u201callow\u201d to mean that computer resources or controls provide a service. Instead of writing \u201cMy NCBI allows users to store searches\u201d, write \u201cMy NCBI stores searches for users\u201d.\nDo not write that a computer \u201ccrunches\u201d data---\u201cprocesses\u201d, or a similar term, is more appropriate.\nRead about anthropomorphism and think about how computer jargon may relate to it.\nBefore making your Web pages public, have your colleagues, a person naive to the project, and an editor review your pages. Use the most accurate representations of symbols, with consideration of the capabilities of various Web browsers. Consider layout and color, as well as content, as means of making your ideas understandable and engaging.\nConstructing Searchable Web Pages\nAll static and dynamically generated Web pages on public servers must be designed to maximize usability and searchability. HTML documents must have title and meta tags in the <head> section, and links must be unbroken:\n\n\nTITLE The document title (of 50 characters or fewer, including spaces) must be unique within NCBI. In addition to the document title, consider adding a title attribute to each meaningful image on the page. This is important if you use an image with graphical text as the heading of your page. The title should briefly describe what is in the image. Most visual browsers preferentially show image title text as a tooltip over the image. If the image is absent, the browser uses the ALT tag. If the ALT tag is absent, there is no pop-up. Voice browsers also speak the title tag, if any, or the ALT tag, if any, or nothing. Document titles are displayed on the search results page of a search engine, so the title needs to be human readable and should clearly convey what the page contains.\nAUTHOR Use your group's project name for the author value.\nKEYWORDS Although some search engines do not use keywords, keywords are still helpful in intranet searches, such as the NCBI Site Search. Use no more than 25 single keywords or some combination of 2-3-word phrases that are specific to the content of the page in a comma-delimited list. Think of different ways to describe your content; people often use different words and phrases to search for the same content (e.g., medical school or school of medicine, vitamin C or ascorbic acid). Start with a base of \"national center for biotechnology information, ncbi, national library of medicine, nlm, database, archive\" (searches of keywords are case insensitive) and then add words more specific to the content of your NCBI pages. Use a thesaurus or the Medical SubHeading (MeSH) browser to explore additional keywords, as well as a dictionary to ensure correct spelling and to find common alternate spellings. This approach will be useful for both internet and intranet searches by search engines.\nDESCRIPTION The description, like the title, must be unique. The best descriptions are short and specific sentences with fewer than 25 words, with the most relevant words near the beginning. Descriptions are displayed on the search results page of a search engine.\nLINKS Links may take you out of the present document or take you to another part of the same document. Links out of the document must reference existing content. These links include hyperlink \u201chref\u201d attributes, such as <a href=\u201curi\u201d>label</a>, image src tags, such as <img src=\u201cfoo.jpg\u201d/>, and linked stylesheets and Javascript files, such as <link rel=\u201cstylesheet\u201d type=\u201ctext/css\u201d href=\u201cstyles.css\u201d/> and <link rel=\u201cjavascript\u201d type=\u201ctext/javascript\u201d href=\u201cmyscript.js\u201d/>. All links within the document must refer to existing anchors.\n\n\nTITLE The document title (of 50 characters or fewer, including spaces) must be unique within NCBI. In addition to the document title, consider adding a title attribute to each meaningful image on the page. This is important if you use an image with graphical text as the heading of your page. The title should briefly describe what is in the image. Most visual browsers preferentially show image title text as a tooltip over the image. If the image is absent, the browser uses the ALT tag. If the ALT tag is absent, there is no pop-up. Voice browsers also speak the title tag, if any, or the ALT tag, if any, or nothing. Document titles are displayed on the search results page of a search engine, so the title needs to be human readable and should clearly convey what the page contains.\n\nAUTHOR Use your group's project name for the author value.\n\nKEYWORDS Although some search engines do not use keywords, keywords are still helpful in intranet searches, such as the NCBI Site Search. Use no more than 25 single keywords or some combination of 2-3-word phrases that are specific to the content of the page in a comma-delimited list. Think of different ways to describe your content; people often use different words and phrases to search for the same content (e.g., medical school or school of medicine, vitamin C or ascorbic acid). Start with a base of \"national center for biotechnology information, ncbi, national library of medicine, nlm, database, archive\" (searches of keywords are case insensitive) and then add words more specific to the content of your NCBI pages. Use a thesaurus or the Medical SubHeading (MeSH) browser to explore additional keywords, as well as a dictionary to ensure correct spelling and to find common alternate spellings. This approach will be useful for both internet and intranet searches by search engines.\n\nDESCRIPTION The description, like the title, must be unique. The best descriptions are short and specific sentences with fewer than 25 words, with the most relevant words near the beginning. Descriptions are displayed on the search results page of a search engine.\n\nLINKS Links may take you out of the present document or take you to another part of the same document. Links out of the document must reference existing content. These links include hyperlink \u201chref\u201d attributes, such as <a href=\u201curi\u201d>label</a>, image src tags, such as <img src=\u201cfoo.jpg\u201d/>, and linked stylesheets and Javascript files, such as <link rel=\u201cstylesheet\u201d type=\u201ctext/css\u201d href=\u201cstyles.css\u201d/> and <link rel=\u201cjavascript\u201d type=\u201ctext/javascript\u201d href=\u201cmyscript.js\u201d/>. All links within the document must refer to existing anchors.\n\nExample\n\n<head>\n<title>Single Nucleotide Polymorphism (SNP)</title>\n<meta name=\u201cauthor\u201d content=\u201csnpdev\u201d>\n<meta name=\u201ckeywords\u201d content=\u201cnational center for biotechnology information, ncbi, national library of medicine, nlm, national institutes of health, nih, database, archive, single nucleotide polymorphism, SNP, sequence variation, genome, gene mapping, population structure, dbSNP, evolution, microsatellite repeat, phenotype\u201d>\n<meta name=\u201cdescription\u201d content=\u201cThe Single Nucleotide Polymorphism database (dbSNP) is a public-domain archive for a broad collection of simple genetic polymorphisms.\u201d>\n</head>\nMake sure that the content on your page is visible on browsers that have JavaScript disabled. Not all search engines can index content contained in scripts.\nKeep Your Web Pages Current\nDates are an important part of your Web document because they help readers understand where your information fits in the timeline of relevant events. In some Web documents, dates serve merely to let readers know when the pages were checked. In other Web documents that report on fast-changing information, dates assume more importance.\nWhen information is time sensitive, place the date at the top of the Web document. Otherwise, place the date at the bottom of the page.\nIt is also helpful to distinguish these two types of dates. \u201cLast Updated\u201d conveys some sense of information that is time sensitive, whereas \u201cRevised\u201d seems to suggest more of a \u201cmaintenance\u201d approach. For the sake of consistency in the presentation of these dates, use the following forms:\n\nLast Updated: November 21, 2003.Revised: November 21, 2003.\n\nLast Updated: November 21, 2003.\nRevised: November 21, 2003.\nWhen using \u201cLast Updated\u201d, place the date at the top of the Web document. When using \u201cRevised\u201d, place the date at the bottom of the page.\nNote the periods at the end of the entries.\nGlossaries on the Web\nThere are two styles for glossaries on the NCBI Web pages:\n\nword to be defined - fragment and/or sentence definition.\n\nword to be defined\n\u2003\u2003fragment and/or sentence definition.\nThe first one saves a little space, if the definition is short enough. Note that both definitions begin with a lowercase letter and end with a period.\nItemized Lists\nMany NCBI Web pages contain itemized lists. It is important to consider the elements of an itemized list and then decide on the type of list that you will need. For more information, also see Lists in Style Points and Conventions.\nThere are three considerations for making lists:\n\nType of list: Is the order of the list items important? (If Yes, use a Numbered List; if No, use a Bulleted List.)\n\nWhether list items are fragments or complete sentences: Will the list items be fragments or complete sentences? (Sentence-style punctuation is used for complete sentences.)\n\nCapitalization: When should list items be capitalized? (Action verbs that begin lists and lists that follow headings without additional explanatory text begin with capital letters.)\nBelow are six examples of the two types of lists. There are two style choices in the Numbered List and four style choices in the Bulleted List. Please apply your style choice to your Web document consistently.\nNumbered List\nIn a Numbered List, the order of execution of the items is important and/or emphasis on the number of items is being made.\nWhen providing instructions or directions that must be followed in a particular order, capitalize the first word of the entry and end it with a period. Each item of this list begins with an \u201caction\u201d verb (sometimes called \u201ccommands\u201d), meaning that the person reading the list is being told what to do and must take action to get the wanted results. See Example 1.\n\nExample 1:\n\nPress the Validate and Continue button.\nEnter the number of CDS features.\nScroll down to the CDS Feature box.\nComplete the CDS Feature subsections.\nWhen the items in the list are not complete sentences, no punctuation is used at the ends of the items. See Example 2.\n\nExample 2:\n\nFor each complete submission you have made to us, you will receive by email:\nan automatic preliminary GenBank flatfile\na GenBank Accession number\na completed GenBank flatfile\nBulleted List\nIn a Bulleted List, the order of execution of the items is not important (it is not a step-by-step procedure), and \u201ccounting\u201d the items is not necessary.\nIn both Examples 3 and 4 that follow, the list items merely continue the idea of the introductory sentence fragment. Contrast the use of the verbs in Example 4 with the action verbs in the Numbered List, Example 1. Note that these verbs in Example 4 are not capitalized because they are not giving directions for actions as commands. Note also that there are no periods, semicolons, or commas at the ends of the entries in Examples 3 and 4, because each item entry presents a part of the thought (each item entry is only a part of the whole idea, with the \u201cidea\u201d being the introduction to the list by the introductory sentence fragment and the list entries themselves). Because of the layout of the list itself, ending punctuation is not needed; the list presents the idea clearly.\n\nExample 3:\n\nUse BankIt if:\n\nyou have one or a few sequence submissionsyou prefer to use a WWW-based submission toolyour sequence annotation is not complicatedyou do not require sequence analysis tools to submit your sequence(s)\n\nyou have one or a few sequence submissions\nyou prefer to use a WWW-based submission tool\nyour sequence annotation is not complicated\nyou do not require sequence analysis tools to submit your sequence(s)\n\nExample 4:\n\nFailure to recognize foreign segments in a sequence can:\n\nlead to erroneous conclusions about the biological significance of the sequencewaste time and effort in analysis of contaminated sequencedelay the release of the sequence in a public databasepollute public databases with contaminated sequence\n\nlead to erroneous conclusions about the biological significance of the sequence\nwaste time and effort in analysis of contaminated sequence\ndelay the release of the sequence in a public database\npollute public databases with contaminated sequence\nWhen a list of complete sentences immediately follows a heading, use paragraph indents with filled bullets at the first level. (Your Browser may control the types of symbols used with nesting.) Begin with a capital letter and end the sentence with a period. See Example 5.\n\nExample 5:\n\nBankIt: GenBank Submission by WWW\n\nGenBank provides annotation examples and descriptions for several types of sequence submissions.Each sequence must be submitted individually and will receive its own BankIt number.\n\nGenBank provides annotation examples and descriptions for several types of sequence submissions.\nEach sequence must be submitted individually and will receive its own BankIt number.\nWhen a list of fragments immediately follows a heading, use paragraph indents with filled bullets. Begin with a capital letter and do not use periods, semicolons, or commas as closing punctuation for the fragments. A combination of fragments and complete sentences is fine. If a complete sentence is used, use a closing period. See Example 6 for use of this combined form.\n\nExample 6:\n\nRequirements for Every Submission\n\nContact informationRelease data informationInput DNA sequenceA contiguous nucleotide sequence of at least 50 base pairsType of molecule sequencedDescription of the sequence:Click on the specific examples in the left column.If the sequence submitted does not fall into one of the categories on the left, please use the available features or provide a complete description.\n\nContact information\nRelease data information\nInput DNA sequence\nA contiguous nucleotide sequence of at least 50 base pairs\nType of molecule sequenced\nDescription of the sequence:\nClick on the specific examples in the left column.\nIf the sequence submitted does not fall into one of the categories on the left, please use the available features or provide a complete description.\nOutlines in Web Help Documents\nThere are many ways to present information clearly and effectively. Consider using an outline when writing your Web Help documents. If you do plan on using an outline, an outline at the beginning of your Web Help document is a good way to orient your readers so that they can quickly understand the layout of your information. An outline is another visual aid to supplement the information supplied by the sidebars and toolbars. One good outline method, shown below, uses an indent system shown with specific symbols at each level of indent, a system used by Word and other wordprocessors.\nThis is an example of the indent system:\n\nOverviewPubmed SearchesAuthor Names\n\nOverview\nPubmed Searches\nAuthor Names\nAn alternative method uses a combination of numbers and symbols:\nOverview\nPubMed Searches\nAuthor Names\nBoth methods present Help documentation clearly and effectively.\nMany people will print out documents to read off-screen. Unless the outline is on a Web page by itself, the assumption is that all of the material contained in the Outline will print out as one document. If sections of the Outline are links to other pages, add a parenthetical statement to the Outline section, such as \u201c(open and print this link separately)\u201d. Note that the words are lowercase. In general in Outlines, use lowercase for parenthetical information. A good example of this is shown on the OMIM Help page.\nWeb Pages without Reference Lists: Making Citations\nLink every citation in the text to PubMed, PubMed Central, and Bookshelf, where possible. Where this is not possible, all information must be provided for the reader in National Library of Medicine (NLM) format:\n\n ... was described previously (Lipman et al. 2002; Benson et al. 2000) (Abramovitz et al. Chemosphere 1990;21:1221-1229) (Salton G. Automatic text processing. Reading (MA): Addison-Wesley; 1989).\n\n ... was described previously (Lipman et al. 2002; Benson et al. 2000) (Abramovitz et al. Chemosphere 1990;21:1221-1229) (Salton G. Automatic text processing. Reading (MA): Addison-Wesley; 1989).\nIn the example above, both the Lipman journal citation and the Benson journal citation are linked to PubMed. The journal article by Abramovitz is not in PubMed, but enough information is given in this format for the reader to find it from other sources. Likewise, the book by Salton contains enough information for the reader to contact the publisher or bookseller. When a reference list is not being provided on the Web page, complete citations must be provided in the text itself. The four citations given in the sample above are separated because of punctuation issues and concern for readers to be able to more easily understand the amount of information presented with the citations.\nNCBI Standard Abbreviations and Frequently Used Word Forms\nNCBI has an international audience of all educational levels. As an author, you must consider your audience, meaning that if you are presenting a biology paper of great complexity that is not likely to be read by a general audience, it is probably not necessary to write out DNA. If there is any doubt, a good method would be to provide the written-out form of the word, followed by the abbreviated form in parentheses:\n\n ... is called deoxyribonucleic acid (DNA).\n\n ... is called deoxyribonucleic acid (DNA).\nThereafter, use the abbreviated form only. Begin with your written-out forms again for every page that loads on the Web site, unless the pages that follow are a clear continuation of the initial page. Obviously, you must use your judgment on this.\nFrequently Used Word Forms\n\na, an - article used according to the sound of the abbreviation (e.g., an STS; a sequence tagged site); this style point is an exception to the CBE rule, which states that the article is used according to the sound of the written-out form.\nJump to: [A-E]\n[D-F]\n[G-L]\n[M-O]\n[P-R]\n[S-Z]\n\n[A-E]\n\nAIDSLINE - AIDSTrials.\n\nASN.1\n\n\nAVLINE\n\n\nBAC-end sequence - (note hyphen).\n\nBankIt\n\n\nbase pair - (two words).\n\nBLAST - PHI-BLAST, PSI-BLAST, QBLAST, RPS-BLAST, IgBLAST, MegaBLAST.\n\nBLink - BLAST link.\n\nBLOSUM62\n\n\nBookshelf\n\n\nBoolean - (capitalized).\n\nby-product(s)\n\n\nC terminus, COOH terminus, C-terminal\n\n\ncatalog - (no \u201c-ue\u201d).\n\nCATLINE\n\n\nCCAP - Cancer Chromosome Aberration Project.\n\nCD-Search\n\n\nCDD - Conserved Domain Database.\n\nCGAP - Cancer Genome Anatomy Project.\n\nCGH - comparative genomic hybridization.\n\ncheck box\n\n\nChemID plus\n\n\ncis - (italic).\n\nClinicalTrials.gov\n\n\nClustalW\n\n\nCn3D\n\n\nco - co-dominant, co-inheritance, co-segregation, cofactor, cooperative.\n\nCOGnitor\n\n\nCOGs - Clusters of Orthologous Groups.\n\ncross - crossing-over (recombination); but crossover (events), crossovers, crosslink, crossbreeding.\n\ncutoff - (noun).\n\ncut off - (verb).\n[D-F]\n\n3D - (for three-dimensional; not 3-D).\n\nDART - Domain Architectural Retrieval Tool.\n\ndata - this is a plural word (datum is singular).\n\ndatabase-mining\n\n\ndataset\n\n\ndbEST\n\n\ndbGSS\n\n\ndbSNP\n\n\ndbSTS\n\n\nDDBJ\n\n\nDDBJ/EMBL/GenBank - (alphabetical order as agreed by collaborators).\n\nDDD - Digital Differential Display.\n\nDGED - Differential Gene Expression Displayer.\n\ndrop-down menu\n\n\nemail - consider putting the email address in boldface text.\n\n\nEMBL\n\n\nemploys - change to \u201cuses\u201d unless specifically referring to the employment of a person.\n\nEntrez\n\n\nEntrez Genomes\n\n\nEntrez Nucleotides\n\n\nEST - expressed sequence tag.\n\neukaryote - (no \u201cc\u201d).\n\nExPASy\n\n\nfa2htgs - not to be capitalized, even beginning a sentence.\n\nfalse-positive results\n\n\nFASTA\n\n\nFISH - fluorescence in situ hybridization.\n\nflatfile - (one word).\n\nfruit fly\n\n\nFTP\n\n[G-L]\n\nGDS - GEO DataSets.\n\nGenBank\n\n\nGeneMap\u201999\n\n\nGenPept\n\n\nGEO - Gene Expression Omnibus.\n\nGI - \u201cGeninfo Identifier\u201d.\n\nGLS - Gene Library Summarizer\n\nHelp desk - NCBI Help desk\n\nhomepage\n\n\nhomolog - (no \u201c-ue\u201d) .\n\nHomoloGene\n\n\nHuman\u2013Mouse Homology - (note en dash).\n\nID - sequence ID, PubMed ID, MEDLINE UID.\n\nin vitro\n- (italic).\n\nin vivo - (italic).\n\nkb - kilobase.\n\nLOCATORplus\n\n\nLocusLink\n\n\nlog in - (verb).\n\nlogin - (noun).\n\nlook-up table\n\n\nlowercase - (one word).\n[M-O]\n\nMAGEML - MicroArray Gene Expression Markup Language.\n\nMap Viewer\n\n\nmatrices\n\n\nMb - megabase.\n\nMD - (no spaces, no periods; \u201cMedical Doctor\u201d).\n\nMEDLINE\n\n\nMEDLINEplus\n\n\nMGC - Mammalian Gene Collection.\n\nMGD - Mouse Genome Database.\n\nMGED - Microarray Gene Expression Database.\n\nMinSeq - Minimal Sequence.\n\nMMDB - Molecular Modeling Database.\n\nModel Maker\n\n\nmulti - multi-step.\n\nN terminus, NH\n2\nterminus, N-terminal\n\n\nNEXUS\n\n\nNLM Gateway\n\n\nnon - non-coding, non-cumulative, non-identical, non-redundant, non-synonymous, nonhuman.\n\nOLDMEDLINE\n\n\nOMIM\n\n\nonline\n\n\nONO - order and orientation information\n\n[P-R]\n\npairwise\n\n\nparalog - (no \u201c-ue\u201d).\n\nPDB - Protein Data Bank (Brookhaven).\n\nPDBeast\n\n\nPfam\n\n\nPhD - (no spaces, no periods).\n\nPHYLIP\n\n\nPopSet\n\n\npost - post-translational.\n\npre - precalculate, precomputed, predetermine, pre-existing.\n\nPREMEDLINE\n\n\nProbeSet\n\n\nprokaryote - (no \u201cc\u201d).\n\nPROW - Protein Reviews On the Web.\n\npsort2\n\n\nPSSM - position-specific scoring matrix.\n\nPubMed\n\n\nPubMed Central\n\n\npull-down menu\n\n\nRCSB - Research Collaboratory for Structural Bioinformatics.\n\nRefSeq - Reference Sequence.\n\nRepeatMasker\n\n\nRFLP - restriction fragment length polymorphism.\n[S-Z]\n\nSAGE - serial analysis of gene expression.\n\nSAGEmap\n\n\nSequin\n\n\nSERLINE\n\n\nSKY/CGH - Spectral Karyotyping and Comparative Genomic Hybridization database.\n\nSMART\n\n\nSNP - single nucleotide polymorphism.\n\nSOFT - Simple Omnibus Format in Text.\n\nspecies - spp. (plural; note period).\n\nSpidey\n\n\nSSLP - simple sequence length polymorphism.\n\nstand-alone program - (note hyphen).\n\nSTS - sequence tagged site.\n\nSWISS-PROT\n\n\nTaxBlast\n\n\nTaxonomy Browser\n\n\nTaxPlot\n\n\ntbl2asn - not to capitalized, even beginning a sentence.\n\n\nTinySeq - Tiny Sequence.\n\nToolKit\n\n\nToolBox\n\n\ntrans - (italic).\n\nUniGene\n\n\nUniSTS\n\n\nUniVec\n\n\nuppercase - (one word).\n\nUserID\n\n\nVAST - Vector Alignment Search Tool.\n\nVecScreen\n\n\nversus - (italic); OK to abbreviate as \u201cvs.\u201d in tables.\n\nVNTR - variable number of tandem repeats.\n\nwebsite\n\n\nWhole Genome Shotgun sequencing\n\n\nwild card\n\n\nXML\n\n\nxProfiler\n\n\nX-ray\n\n\nZFIN - Zebrafish Information.\nBe consistent with these frequently used word forms.", "pairs": [], "interleaved": []}