Web Site to assist with becoming a provider
- Home page for providers
Provider Motivations NOT to support
The following has become apparent from dialogs with some providers:
- They are not willing to spend money to get a suitable file created
- They do not have programming staff to code, i.e. they will need to hire a developer.
- They do not want to have their advice question by allowing second or third opinions of what people should take.
- Often they perceive this as generating support calls (paying more staff) dealing with customers’ questions
- Their business model depend on up-selling probiotics (huge profit margins), supplements, or meal plan. Customers getting second or third opinions risk lost of these profits
- Pure Ego issues.
Directly sending the file
This should only be done by their client (owner of the microbiome sample) from the provider site. This simplifies the transfer (more client friendly) and usually results in good will for the provider (as well as repeat business). Many people have switched to supported providers for subsequent tests because they wish to use the features on the Microbiome Prescription site.
The simplest format is a very very simple upload (post) a text file consisting of nothing more than:
Line 1: Email Address of user
Line 2-N: NCBI Taxon Number, Percentage
That is it!!! We have a test page available for people who wish to try it (data is not saved).
When you wish to enable it so that it is saved, we will provide a key to you so that we know where the data is coming from. THERE IS NO COST. See statistics on uploads here.
This also clarifies to users whether they should or could be seeing a specific species, genus or family on their report.
Route 1: Giving the client a file to download and then upload
This may be as simple as a CSV file illustrated below, or rich in other data. Once we have a sample of the file, we will code an import routine (no cost to the provider).
Line 1-N: NCBI Taxon Number, Percentage
356, 0.004 468, 0.002 469, 0.002 506, 0.373 543, 0.338 551, 0.002 561, 0.311 562, 0.025 613, 0.019 712, 0.05 713, 0.002 724, 0.0429 729, 0.0429 766, 0.003 775, 0.003 780, 0.003 815, 35.804 816, 35.804 817, 0.002 818, 4.764 820, 4.165 821, 0.011 823, 3.028 830, 0.002 836, 0.015 838, 0.032 841, 2.608 853, 11.933 872, 0.039 904, 0.025 905, 0.025 906, 0.008 970, 0.045 976, 46.664 1030, 0.018 1046, 0.002 1047, 0.002 1051, 0.002
Why NCBI Numbers?
The reasons are simple:
- various bacteria have dozens of names — on occasion, the name was deprecated and assigned to a different bacteria. It assures us that we have the right bacteria.
- We use the KEGG: Kyoto Encyclopedia of Genes and Genomes, and their data is all keyed to NCBI Taxon numbers
- It allows data to be stored in a more compact fashion (up to 60x smaller database) and allows faster processing of data (saving operating costs).
Alternative: Use the NCBI Names
We have 3,635,527 names from NCBI in our database and can do a lookup of NCBI numbers by name. This is less precise — however, some providers use this route with over 99% of their names matching.
We request all taxonomic ranks to be specified
Our experience is that percentages become distorted (under reported) when we rollup from species to genus to family etc. Typically, there will be some undetermined species in each genus, family, etc. These will often be referred to as “unclassified Lactobacillus” etc.
Example of a walk thru complete test file:Example of CSV file to be pasted
A download will start
The file will show the NAME for each of the taxon, so you can verify that the numbers are correct.