Chapter 2 Input Data Format
The online tool requires 3 kinds of inputs: Disorder Type, NBS Program, and Metabolic Information.
2.1 Disorder Type
Disorder type can be specified by choosing the corresponding item on the sidebar. There are four disorders included in the application currently: GA-1(Glutaric Acidemia Type I), MMA(Methylmalonic Acidemia), OTCD(Ornithine transcarbamylase deficiency), and VLCADD(Very Long-chain Acyl-CoA Dehydrogenase Deficiency).
2.2 NBS Program
NBS program, which indicates the place where the data is collected from, can be specified by choosing the corresponding item on the sidebar.
The current model is based on data from California. Different states or countries may have different NBS programs, the model may not fit the data outside of California. Please contact us if you would like to cooperate with our team and include the model for your state or country.
2.3 Metabolic Information
The input data file could be in a comma separated values (csv) format, or in a plain text format with its delimiters being one of the following: semicolon, tab, or space. The first row of the file contains the header information for each column. Each row after the header contains the corresponding information of each sample. The description and format of each column are described below. The headers are case insensitive. As long as all the 39 marker levels are included in the file, they can be in any order depending on your preference.
| Column | 1 | 2-40 |
|---|---|---|
| Headers | id | Original marker name or its abbreviation |
| Example Headers | ID, sample | Citrulline, cit, C18:1, c181, C5-OH, C5OH |
| Values | Unique sample id (string) | Individual marker concentration levels (numeric) |
| Example Values | S01, sample_001 | 0.2, 0.11421383 |
2.4 A Full List of Acceptable Header Fields
This table aims to list all the headers, and describe the alternatives that are acceptable in the application.
| Headers | Possible Alternatives |
|---|---|
| id | ID, SAMPLE, SAMPLE IDENTIFIER, SAMPLE ID, SID, IDENTIFIER |
| GLY | GLY, GLYCINE |
| ALA | ALA, ALANINE |
| PRO | PRO, PROLINE |
| VAL | VAL, VALINE |
| OXP | OXP, 5-OXOPROLINE, pyroglutamic acid, GLP |
| XLE | XLE, LEU-ILE, LEU+ILE, LEUCINE+ISOLEUCINE, LEUCINE AND ISOLEUCINE, LEUCINE OR ISOLEUCINE |
| ORN | ORN, ORNITHINE |
| MET | MET, METHIONINE |
| ARG | ARG, ARGININE |
| CIT | CIT, CITRULLINE |
| PHE | PHE, PHENYLALANINE |
| TYR | TYR, TYROSINE |
| C0 | C0, FREE CARNITINE, FC |
| C2 | C02, C2 |
| C3 | C03, C3 |
| C4 | C04, C4 |
| C5:1 | C051, C51, C5:1 |
| C5 | C05, C5 |
| C6 | C06, C6 |
| C8:1 | C081, C8:1, C81 |
| C8 | C08, C8 |
| C10:1 | C101, C10:1 |
| C10 | C10 |
| C12:1 | C121, C12:1 |
| C12 | C12 |
| C14:1 | C141, C14:1 |
| C14 | C14 |
| C14OH | C14OH, C14-OH |
| C16:1 | C161, C16:1 |
| C16 | C16 |
| C16OH | C16OH, C16-OH |
| C18:2 | C182, C18:2 |
| C18:1 | C181, C18:1 |
| C18 | C18 |
| C18:1OH | C181OH, C18:1OH, C18:1-OH |
| C18OH | C18OH, C18-OH |
| C5OH | C05OH, C5OH, C5-OH |
| C3DC | C03DC, C3DC, C3-DC |
| C5DC | C05DC, C5DC, C5-DC |