[Dictionary 20251002-1, pre-release for testing purpose - many rules are still being added and/or refined]
Background:
MosaicDX Organic Acids Test (OAT) is a very useful panel [example download] for evaluating catabolic energy metabolism and other key pathways over a defined fasting period + sleep. However, manual interpretation of these reports requires a skill-set and/or billing schedule that is out-of-scope for many point-of-care scenarios. There are known issues where if specimens thaw in transit, are delayed or when creatinine is sufficiently out-of-range, these problems can cause a left or right shift to many values. These reports also lack inferences for intracellular coenzyme, electrolyte and mineral status, which can be provided by the array of analytes reported.
Current features:
1) Client-side javascript extracts the analytes, values and ranges from pages 1-6 of an unmodified (English, 2023-2025 layout) MosaicDX OAT results PDF, displays them on-screen with a LOW, IN-RANGE LOW, IN-RANGE HIGH, HIGH status, Deviation% and provides a download function as CSV that includes a large number of additional columns.
2) The parsing / extraction has a configurable start/end page, for where PDF reports have been sliced up and there are page ranges missing, meaning the actual page numbers no longer match the page numbers indicated in the footer of each page.
3) Left or right shift in results, when identified, can be manually compensated for by adjusting the Shift Correction% input field +/- from 100%. A left-shift score is calculated in the totals. Total scores of 50% or above in Req_ShiftCorr suggests shift correction may be appropriate. A common left-shift correction value may be around 150%.
4) The extracted LOW and IR-LOW analyte values and dictionary-based rules score required cofactors (as coenzymes / minerals /
electrolytes, etc) and the sum of these scores are displayed below the table, compared to the total possible score and displayed as a percentage. The higher confidence percentage,
the more confidence in a specific cofactor deficiency is provided. Currently, a confidence score above 30% should be treated as a progressively positive indication of deficiency. This will be refined in future updates, when mitochondrial and cytosolic cofactors are separated.
Upstream reactions can also be included as required cofactors, with
lower 'weights' recorded.
5) A default dictionary is installed (and being further improved). While I'd encourage people to share any rules / patterns they'd like to include, your own personal dictionary file can also be used. You can download and
extend the existing dictionary schema by adding columns labelled
"Req_<cofactor>" and these will be included in the calculations /
total. Additional rules can also be defined in the dictionary file,
evaluating the variance between the Deviation% of 2 analytes, against a threshold%. If this is exceeded, the rule status is set to TRUE and is included in
the total flags for cofactors. ie. if Succinic : Fumaric acid ratio is elevated, FAD, Fe, S, CoQ10 are flagged as potentially low. If the rule's Analyte#2 is "0", the variance% is calculated against ideal (0%). This allows for rules to be created against a single analyte's value.
Notes:
1) A deficiency of one redox currency state, eg. NADP implies an excess of the other state, eg. NADPH.
2) Indicated acetyl-CoA deficiency without indicated CoA deficiency suggests glycogen homeostasis / fatty acid oxidation issues.
3) Fe, O2 and antioxidant (Vitamin C /BH4) are used as cofactors in the same hydroxylase reactions, meaning that a deficiency in any 1 of these can impair the reaction and confound the deficiency results for the others. Interpret with caution.
4) Mobile UI portrait mode support is limited, due to rich table content. Javascript must be enabled in your browser for this tool to work.
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Disclaimer:
MosaicDX and ‘OAT’ are used nominatively to identify the compatible PDF
report. Born Free is not affiliated with, endorsed by, or sponsored by MosaicDX. For support with MosaicDX’s official reports, contact MosaicDX directly; this tool is community-built and independent.
Information is general and not medical advice. Outputs are experimental and may contain errors. Do not use for diagnosis or clinical decisions; seek advice from a qualified health professional. This tool is provided for research/education to help read report PDFs. It is not intended to diagnose, treat, prevent or monitor disease, and is not intended for clinical decision-support. If you use software for such purposes, you are responsible for complying with applicable regulations.
This tool is provided ‘as is’: we don’t warrant completeness or accuracy and exclude all implied warranties to the maximum extent permitted by law.