Question: I have generated some phenotype data that I would like to put into GeneNetwork. How should I name my traits?
Answer: Phenotype trait names in GeneNetwork should have this general form when possible:
- Your description should start with very short list of "approved" general category and ontology terms. These terms are used to subdivide the entire collection of phenotypes by system, organ, or level of analysis. Some examples may help: "Central nervous system", "Immune system", "Metabolism", "Development", or "Urogenital system". Capitalize this list as you would a standard English sentence. Separate terms by commas and then end the terms with a colon. For example, "Central nervous system, pharmacology, endocrinology:" is a valid set of three terms. These terms do not really describe your trait, but are used by you and other users to figure out how many traits there are in specific categories.
Before making up your own terms, please review the current terms in GeneNetwork and find some terms/ontology categories that look good to you. If you have questions contact one of us on the GeneNetwork development team.
- After the colon start with your description of the phenotype you have generated. For example: "Ethanol response..." or "Anxiety assay...", "Brain weight...". The first letter should almost always be capitalized.
- Do not start with a generic uninformative word such as "Mean", "Maximum", "Mechanical", "Count", "Number", "Difference", "Baseline", "Induction", "Decrease", "New", "Adjusted", "Distance", "Right", "Left", "Bilateral", "Time", "Total", "Percentage", "Percent". The reason is that the traits should be alphabetized and categorized in a conceptually useful way; not by something "dumb" like the "total" or "percent".
- Do not start with a specific instrumental assay such as "Morris water maze" or "Dowel test..." or "Porsolt test behavior". Many of these tests will be unknown to other users. Try to use a term that reflects the intent of the assay (Motor coordination test, Learning and memory assay, Allergic airway response). This may be difficult, particularly for tests such as the Porsolt swim test and the Morris water maze that measure aspects of many different traits (anxiety, activity level, spatial navigation, visual acuity etc). But in the interest of clarity of intent rather than precision of measurement, please follow this suggestion. The actual assay instrument can be listed after the primary and secondary trait descriptions.
- Many traits can be difficult to categorize in a consistent way. For example a trait such as "ventral midbrain copper level in males" could be labeled "copper level in the ventral midbrain." There is no right or wrong way to do this, but the convention should be to choose the order that you think will be most useful to other users in terms of comprehension and consistency with other existing phenotypes. Review related phenotypes before you start naming your own. You will find good and bad examples.
- Dose and route of drug delivery. If the phenotype is a pharmacological phenotype, whenever practical enter the doses and routes of injection in parentheses after the name of the general trait. For example, "Cocaine response (40 mg/kg ip)". We would prefer to use "ip" and "iv" rather than i.p. and i.v., but this is not a strong preference. If a protocol requires multiple treatments, please include them if possible. For example, "Cocaine response (3 x 3.2 mg/kg ip, Days 2, 3, 4),...").
- Series of more precise definitions of the phenotype and the subject(s) will often follow with commas used as separators. If possible make this understandable to almost any user, even at the risk of being wordy.
For example, "Cocaine response (3 x 3.2 mg/kg ip, Days 2, 3, and 4), conditioned place preference (CPP), change in time in cocaine-paired compartment relative to baseline (Day 5 minus Day 1) for 50 to 90-day-old males and females [sec]"
- Sex. If the data are for males please write out "in males" or "of male" or "for males". Do not just add a comma such as " , males" or "(M)". This should usually go at the end of the description.
- Age and condition of subjects can be added if you think it is essential or helpful. However, do not bother with a generic addition "adult" since that is what most users will reasonably assume. If you would like to add an age range then use this format "in 100 to 200-day-old males and females" or "of 3 to 4-month-old males".
- Mandatory units of measurement between square brackets [min] or [sec] or [n bream breaks/10 min test]. If you are using an ordinal scale, then describe the scale within the brackets. If the units are simply a ratio or percentage then use [ratio] or [%].
Other advice on trait descriptions:
- Do Not Capitalize Each Word in a Description. (e.g, Ethanol Response, Distance traveled after saline - Distance traveled after ethanol for males and females [cm in a 0-5 min test period] )
- Do not use "-" as a minus sign. The dash is too confusing and may sometimes be used as a hyphen. Spell out "minus"
- No not use ALL CAP in a trait description (e.g., TOTAL)
- Do use commas when appropriate. For example, Morphine response severity of abdominal constriction for males needs a comma between "response" and "severity"
- Do not use extraneous words such as "time SPENT on rotarod". "time on rotarod" is good enough.
- Do not start with text or abbreviations that will not be understandable to all users, such as "RSS female and male..."
- Please us a space between a number and the units: Prepulse inhibition at 70 dB for females (not 70db). Please use the correct form of the abbreviation.
- Use American spelling. [RWW, September 10, 2009]
Examples of accepted phenotype descriptions: (by Amelie Baud. Wellcome Trust Centre for Human Genetics, Oxford, UK.)
- Central nervous system, behavior: Anxiety assay, locomotor activity in novel cage between minutes 25 and 30 in novel cage, normalized by Box-Cox transformation [cm]
- Metabolism: Glycemia (intraperitoneal glucose tolerance test), area under the curve between minutes 0 and 120 after injection, normalized by Box-Cox transformation [mM.min-1]