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Mark Andrew Miller turbomam

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Software Developer at the Lawrence Berkeley National Laboratory. Harmonizing biomedical semantics and metadata. Microbiomes, samples, multi-omics.

18 followers · 1 following

Lawrence Berkeley National Laboratory
Philadelphia, PA, USA
07:29 - 4h behind
https://berkeleybop.github.io/people/mark-a-miller/
https://stackoverflow.com/users/3860847/mark-miller
https://orcid.org/0000-0001-9076-6066
in/mamillerpa

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llm-github Public

llm-github/

Python 3
schemas-for-schemaless Public

Illustrations for ICBO 2021 submission

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example-runner-sandbox Public archive

A place to learn about linkml-run-examples. Brought to you by the LinkML Cookiecutter.

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biosample-basex Public archive

Using the Base-X XML database to discover structure in NCBI's Biosample database

Jupyter Notebook 1
synbio-alignments Public

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Python 1
hident Public archive

convert an unordered list of ontology terms into a ordered list, with leading whitespace to indicate heirarchy

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3,033 contributions in the last year

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Activity overview

Contributed to microbiomedata/external-metadata-awareness, microbiomedata/nmdc-schema, microbiomedata/submission-schema and 47 other repositories

Contribution activity

April 2025

Created 93 commits in 6 repositories

Created a pull request in microbiomedata/nmdc-schema that received 9 comments

audit/normalization of prefixes and comments

+801 −630 lines changed • 9 comments

Opened 23 other pull requests in 4 repositories

microbiomedata/external-metadata-awareness 19 merged

some units cleanup
This contribution was made on Apr 10
ucum mapping and merging done
This contribution was made on Apr 10
consistent column count?
This contribution was made on Apr 8
remove "or" column
This contribution was made on Apr 8
acknowledge the separator
This contribution was made on Apr 8
curated MIxS preferred units to UCUM conversions
This contribution was made on Apr 8
Optimize Mongo inserts using Arrow-native batch conversion and insert_many
This contribution was made on Apr 8
sra metadata loading outside of perlmutter
This contribution was made on Apr 8
measurement exploration
This contribution was made on Apr 5
schema flattening script with output
This contribution was made on Apr 3
normalize-measurements target creation and env_triads refinements
This contribution was made on Apr 1
Env triads Makefile target
This contribution was made on Apr 1
Standardize all cache expiration to 30 days using datetime.timedelta
This contribution was made on Apr 1
Rename directories with underscores to hyphens for consistency and add more script aliases
This contribution was made on Apr 1
make better use of pyproject.toml aliases
This contribution was made on Apr 1
Final env triads col plus measurements
This contribution was made on Apr 1
Merge pull request #150 from microbiomedata/main
This contribution was made on Apr 1
backmerge main into improved splitting parsing branch, then close if possible
This contribution was made on Apr 1
Final env_triads collection. Start on biosamples_measurements
This contribution was made on Apr 1

microbiomedata/nmdc-schema 1 merged 1 open

update jinja2 for failing dependabot PR 2361
This contribution was made on Apr 10
ensure mixs_env_triad_field annotations
This contribution was made on Apr 9

berkeleybop/metpo 1 merged

N4L table parsing
This contribution was made on Apr 11

GenomicsStandardsConsortium/mixs 1 open

linting workarounds and docs
This contribution was made on Apr 9

Reviewed 6 pull requests in 3 repositories

GenomicsStandardsConsortium/mixs 4 pull requests

Replace misrepresented string_serialization with structured_pattern – batch 1
This contribution was made on Apr 9
606 mixs editing workflow and policy
This contribution was made on Apr 2
Example added to air temperature
This contribution was made on Apr 2
Update CONTRIBUTING.md
This contribution was made on Apr 2

microbiomedata/nmdc-schema 1 pull request

Add more range constraints to match range implied by structured_patterns.
This contribution was made on Apr 9

linkml/linkml 1 pull request

linter config schema and python with exclude_type
This contribution was made on Apr 7

Created an issue in microbiomedata/submission-schema that received 5 comments

start writing some prototype UCUM validation patterns

based on mixs-prefunit-slots-to-ucum.tsv from external-metadata-awareness

5 comments

Opened 29 other issues in 3 repositories

microbiomedata/nmdc-schema 20 open

some structured_patterns result in materialized patterns that have two caret anchors ^^
This contribution was made on Apr 9
Migration capability limited when no adapter is specified
This contribution was made on Apr 9
Numerous modules/classes/functions have no tests
This contribution was made on Apr 9
lingering example.org-based prefix expansions
This contribution was made on Apr 9
src/schema/core.yaml has a UUID-prefixes example. What is NMDC's preferred prefix for UUIDs?
This contribution was made on Apr 9
src/schema/core.yaml has a IGSN-prefixed example, but igsn is NMDC' preferred prefix
This contribution was made on Apr 9
src/schema/core.yaml uses unresolvable NCBI-prefixed mappings for taxonomic ranks
This contribution was made on Apr 9
id_prefixes is used sporadically in src/schema/external_identifiers.yaml
This contribution was made on Apr 9
pattern in insdc_secondary_sample_identifiers is incompatible with suggested prefix
This contribution was made on Apr 9
remove commented env_package.pattern or apply as an enum
This contribution was made on Apr 9
remove commented SubstanceRoleEnum.permissible_values
This contribution was made on Apr 9
remove commented StatusEnum.permissible_values
This contribution was made on Apr 9
include these slots in UCUM-inspired units surveys
This contribution was made on Apr 3
soluble_iron_micromol is odd in including its units in its name
This contribution was made on Apr 3
soil_text_measure's description is not compatible with a QuantityValue range
This contribution was made on Apr 3
Improve rendering of non-scalar examples in documentation pages
This contribution was made on Apr 3
implicit grouping slots need definition/documentation or removal from nmdc-schema, and proper casing/underscoring
This contribution was made on Apr 3
grouping-like MIxS section slots used as parent slots need better documentation and switch to underscore delimiting
This contribution was made on Apr 3
room_moist_dam_hist slot should probably have string not integer range
This contribution was made on Apr 3
technical_reps slot should probably have integer not string range
This contribution was made on Apr 3

microbiomedata/external-metadata-awareness 7 open

review commit-able files > 50 MB
This contribution was made on Apr 10
make class_slot_flattening.py metamodel-informed
This contribution was made on Apr 8
identify which slots are measurements
This contribution was made on Apr 4
add tqdm to new_bioportal_curie_mapper.py
This contribution was made on Apr 1
OAK annotate text configuration for whole words only doesn't seem to work
This contribution was made on Apr 1
ignore some annotations like ENVO 'gut' ?
This contribution was made on Apr 1
obsolete flag not present in some annotations anymore?
This contribution was made on Apr 1

berkeleybop/metpo 2 open

Do we need to use SPIN to get value from N4L? TopBraid COmposer?
This contribution was made on Apr 8
N4F license/acknowledgements
This contribution was made on Apr 8

2 contributions in private repositories Apr 1 – Apr 8