adding an deduplicated analysis set that selects a single strain for each experimental condition

README.md

@@ -24,11 +24,150 @@ experimental_conditions:
 doi: https://doi.org/10.15252/msb.20199174
 citation: >-
   Hackett, SR, Baltz, EA, Coram, M, Wranik, BJ, Kim, et al. 2020. Learning causal networks using inducible transcription factors and transcriptome-wide time series. Molecular Systems Biology.
+
+features:
+- applies_to:
+  - hackett_2020
+  - hackett_2020_analysis_set
+  fields:
+  - name: regulator_locus_tag
+    dtype: string
+    description: >-
+      induced transcriptional regulator systematic ID.
+      See hf/BrentLab/yeast_genome_resources
+    role: regulator_identifier
+  - name: regulator_symbol
+    dtype: string
+    description: >-
+      induced transcriptional regulator common name. If no common name exists,
+      then the `regulator_locus_tag` is used.
+    role: regulator_identifier
+- applies_to:
+  - hackett_2020
+  - zev_gev
+  - hackett_2020_analysis_set
+  fields:
+  - name: target_locus_tag
+    dtype: string
+    description: >-
+      The systematic ID of the feature to which the effect/pvalue is assigned.
+      See hf/BrentLab/yeast_genome_resources
+    role: target_identifier
+  - name: target_symbol
+    dtype: string
+    description: >-
+      The common name of the feature to which the effect/pvalue is assigned.
+      If there is no common name, the `target_locus_tag` is used.
+    role: target_identifier
+  - name: time
+    dtype:
+      class_label:
+        names: [0, 2, 5, 7, 8, 10, 12, 15, 20, 30, 45, 60, 90, 100, 120, 180, 290]
+    description: time point (minutes)
+    role: experimental_condition
+  - name: mechanism
+    dtype:
+      class_label:
+        names: ["GEV", "ZEV"]
+    description: Synthetic TF induction system (GEV or ZEV)
+    role: experimental_condition
+    definitions:
+      GEV:
+        perturbation_method:
+          type: inducible_overexpression
+          system: GEV
+          inducer: beta-estradiol
+          description: "Galactose-inducible estrogen receptor-VP16 fusion system"
+      ZEV:
+        perturbation_method:
+          type: inducible_overexpression
+          system: ZEV
+          inducer: beta-estradiol
+          description: "Z3 (synthetic zinc finger)-estrogen receptor-VP16 fusion system"
+  - name: restriction
+    dtype:
+      class_label:
+        names: ["M", "N", "P"]
+    description: >-
+      nutrient limitation, one of P (phosphate limitation (20 mg/l).),
+      N (Nitrogen‐limited cultures were maintained at 40 mg/l ammonium sulfate) or
+      M (Not defined in the paper or on the Calico website)
+    role: experimental_condition
+    definitions:
+      P:
+        media:
+          nitrogen_source:
+            - compound: ammonium_sulfate
+              # Saldanha et al 2004: 5 g/l
+              concentration_percent: 0.5
+          phosphate_source:
+            - compound: potassium_phosphate_monobasic
+              # Hackett et al 2020: 20 mg/l
+              concentration_percent: 0.002
+      N:
+        media:
+          nitrogen_source:
+            - compound: ammonium_sulfate
+              # Hackett et al 2020: 40 mg/l
+              concentration_percent: 0.004
+      M:
+        description: "Not defined in the paper or on the Calico website"
+  - name: date
+    dtype: string
+    description: date performed
+    role: experimental_condition
+  - name: strain
+    dtype: string
+    description: strain name
+    role: experimental_condition
+  - name: green_median
+    dtype: float
+    description: median of green (reference) channel fluorescence
+    role: quantitative_measure
+  - name: red_median
+    dtype: float
+    description: median of red (experimental) channel fluorescence
+    role: quantitative_measure
+  - name: log2_ratio
+    dtype: float
+    description: log2(red / green) subtracting value at time zero
+    role: quantitative_measure
+  - name: log2_cleaned_ratio
+    dtype: float
+    description: Non-specific stress response and prominent outliers removed
+    role: quantitative_measure
+  - name: log2_noise_model
+    dtype: float
+    description: estimated noise standard deviation
+    role: quantitative_measure
+  - name: log2_cleaned_ratio_zth2d
+    dtype: float
+    description: >-
+      cleaned timecourses hard-thresholded based on
+      multiple observations (or last observation) passing the noise model
+    role: quantitative_measure
+  - name: log2_selected_timecourses
+    dtype: float
+    description: >-
+      cleaned timecourses hard-thresholded based on single observations
+      passing noise model and impulse evaluation of biological feasibility
+    role: quantitative_measure
+  - name: log2_shrunken_timecourses
+    dtype: float
+    description: >-
+      selected timecourses with observation-level shrinkage based on
+      local FDR (false discovery rate). Most users of the data will want
+      to use this column.
+    role: quantitative_measure
+  - name: responsive
+    dtype: bool
+    description: >-
+      This labels targets, for a given regulator, with abs(log2_shrunken_timecourses) `>` 0
+
 configs:
   - config_name: hackett_2020
     description: >-
       Microarray expression data comparing cells without estradiol inducer, which express a TF at a very low level and post-induction, which express the TF at a high level by 15-30 minutes post induction. Contains many time points. Cells were grown in minimal medium with glucose in continuous-flow chemostats. In most experiments growth was limited by phosphate limitation.
-    default: true
     dataset_type: annotated_features
     metadata_fields: ["sample_id", "regulator_locus_tag", "regulator_symbol", "time", "mechanism", "restriction", "date", "strain"]
     data_files:
@@ -47,141 +186,43 @@ configs:
             an old unique identifer, for use internally only. Deprecated and will be removed eventually.
             Do not use in analysis. db_id = 0, for GEV and Z3EV, means that those samples are not
             included in the original DB.
-        - name: regulator_locus_tag
-          dtype: string
-          description: >-
-            induced transcriptional regulator systematic ID.
-            See hf/BrentLab/yeast_genome_resources
-          role: regulator_identifier
-        - name: regulator_symbol
-          dtype: string
-          description: >-
-            induced transcriptional regulator common name. If no common name exists,
-            then the `regulator_locus_tag` is used.
-          role: regulator_identifier
-        - name: target_locus_tag
-          dtype: string
-          description: >-
-            The systematic ID of the feature to which the effect/pvalue is assigned.
-            See hf/BrentLab/yeast_genome_resources
-          role: target_identifier
-        - name: target_symbol
-          dtype: string
-          description: >-
-            The common name of the feature to which the effect/pvalue is assigned.
-            If there is no common name, the `target_locus_tag` is used.
-          role: target_identifier
-        - name: time
-          dtype:
-            class_label:
-              names: [0, 2, 5, 7, 8, 10, 12, 15, 20, 30, 45, 60, 90, 100, 120, 180, 290]
-          description: time point (minutes)
-          role: experimental_condition
-        - name: mechanism
-          dtype:
-            class_label:
-              names: ["GEV", "ZEV"]
-          description: Synthetic TF induction system (GEV or ZEV)
-          role: experimental_condition
-          definitions:
-            GEV:
-              perturbation_method:
-                type: inducible_overexpression
-                system: GEV
-                inducer: beta-estradiol
-                description: "Galactose-inducible estrogen receptor-VP16 fusion system"
-            ZEV:
-              perturbation_method:
-                type: inducible_overexpression
-                system: ZEV
-                inducer: beta-estradiol
-                description: "Z3 (synthetic zinc finger)-estrogen receptor-VP16 fusion system"
-        - name: restriction
-          dtype:
-            class_label:
-              names: ["M", "N", "P"]
-          description: >-
-            nutrient limitation, one of P (phosphate limitation (20 mg/l).),
-            N (Nitrogen‐limited cultures were maintained at 40 mg/l ammonium sulfate) or
-            M (Not defined in the paper or on the Calico website)
-          role: experimental_condition
-          definitions:
-            P:
-              media:
-                nitrogen_source:
-                  - compound: ammonium_sulfate
-                    # Saldanha et al 2004: 5 g/l
-                    concentration_percent: 0.5
-                phosphate_source:
-                  - compound: potassium_phosphate_monobasic
-                    # Hackett et al 2020: 20 mg/l
-                    concentration_percent: 0.002
-            N:
-              media:
-                nitrogen_source:
-                  - compound: ammonium_sulfate
-                    # Hackett et al 2020: 40 mg/l
-                    concentration_percent: 0.004
-            M:
-              description: "Not defined in the paper or on the Calico website"
-        - name: date
-          dtype: string
-          description: date performed
-          role: experimental_condition
-        - name: strain
-          dtype: string
-          description: strain name
-          role: experimental_condition
-        - name: green_median
-          dtype: float
-          description: median of green (reference) channel fluorescence
-          role: quantitative_measure
-        - name: red_median
-          dtype: float
-          description: median of red (experimental) channel fluorescence
-          role: quantitative_measure
-        - name: log2_ratio
-          dtype: float
-          description: log2(red / green) subtracting value at time zero
-          role: quantitative_measure
-        - name: log2_cleaned_ratio
-          dtype: float
-          description: Non-specific stress response and prominent outliers removed
-          role: quantitative_measure
-        - name: log2_noise_model
-          dtype: float
-          description: estimated noise standard deviation
-          role: quantitative_measure
-        - name: log2_cleaned_ratio_zth2d
-          dtype: float
-          description: >-
-            cleaned timecourses hard-thresholded based on
-            multiple observations (or last observation) passing the noise model
-          role: quantitative_measure
-        - name: log2_selected_timecourses
-          dtype: float
-          description: >-
-            cleaned timecourses hard-thresholded based on single observations
-            passing noise model and impulse evaluation of biological feasibility
-          role: quantitative_measure
-        - name: log2_shrunken_timecourses
-          dtype: float
+
+  - config_name: hackett_2020_analysis_set
+    description: >-
+      This dataset filters the full data such that a single strain is chosen for each
+      regulator. Where a ZEV with phosphate restriction is available, that is chosen,
+      otherwise a GEV with phosphate restriction is chosen, and if that is not
+      available, then the first available sample is chosen. There are 4 regulators,
+      GCN4, RDS2, SWI1, MAC1, which have multiple replicates of the same conditions.
+      For the time being, these regulators are entirely removed.
+      See `scripts/adding_analysis_set.R`
+    default: true
+    dataset_type: annotated_features
+    metadata_fields: ["sample_id", "regulator_locus_tag", "regulator_symbol", "time", "mechanism", "restriction", "date", "strain"]
+    data_files:
+      - split: train
+        path: hackett_2020_analysis_set.parquet
+    dataset_info:
+      features:
+        - name: sample_id
+          dtype: integer
           description: >-
-            selected timecourses with observation-level shrinkage based on
-            local FDR (false discovery rate). Most users of the data will want
-            to use this column.
-          role: quantitative_measure
-        - name: responsive
-          dtype: bool
+            unique identifier for a specific sample. The sample ID identifies a unique
+            (regulator_locus_tag, time, mechanism, restriction, date, strain) tuple.
+        - name: db_id
+          dtype: integer
           description: >-
-            This labels targets, for a given regulator, with abs(log2_shrunken_timecourses) `>` 0
+            an old unique identifer, for use internally only. Deprecated and will be removed eventually.
+            Do not use in analysis. db_id = 0, for GEV and Z3EV, means that those samples are not
+            included in the original DB.
+
   - config_name: zev_gev
     description: These are the Z3EV and GEV control strains (no specifically tagged TF)
     dataset_type: annotated_features
-    metadata_fields: ["sample_id", "regulator_locus_tag", "regulator_symbol", "time", "mechanism", "restriction", "date", "strain"]
+    metadata_fields: ["sample_id", "time", "mechanism", "restriction", "date", "strain"]
     data_files:
       - split: train
-        path: hackett_2020.parquet
+        path: zev_gev_strains.parquet
     dataset_info:
       features:
         - name: sample_id
@@ -189,120 +230,6 @@ configs:
           description: >-
             unique identifier for a specific sample. The sample ID identifies a unique
             (regulator_locus_tag, time, mechanism, restriction, date, strain) tuple.
-        - name: target_locus_tag
-          dtype: string
-          description: >-
-            The systematic ID of the feature to which the effect/pvalue is assigned.
-            See hf/BrentLab/yeast_genome_resources
-          role: target_identifier
-        - name: target_symbol
-          dtype: string
-          description: >-
-            The common name of the feature to which the effect/pvalue is assigned.
-            If there is no common name, the `target_locus_tag` is used.
-          role: target_identifier
-        - name: time
-          dtype: float
-          description: time point (minutes)
-          role: experimental_condition
-        - name: mechanism
-          dtype:
-            class_label:
-              names: ["GEV", "ZEV"]
-          description: Synthetic TF induction system (GEV or ZEV)
-          role: experimental_condition
-          definitions:
-            GEV:
-              perturbation_method:
-                type: inducible_overexpression
-                system: GEV
-                inducer: beta-estradiol
-                description: "Galactose-inducible estrogen receptor-VP16 fusion system"
-            ZEV:
-              perturbation_method:
-                type: inducible_overexpression
-                system: ZEV
-                inducer: beta-estradiol
-                description: "Z3 (synthetic zinc finger)-estrogen receptor-VP16 fusion system"
-        - name: restriction
-          dtype:
-            class_label:
-              names: ["M", "N", "P"]
-          description: >-
-            nutrient limitation, one of P (phosphate limitation (20 mg/l).),
-            N (Nitrogen‐limited cultures were maintained at 40 mg/l ammonium sulfate) or
-            M (Not defined in the paper or on the Calico website)
-          role: experimental_condition
-          definitions:
-            P:
-              media:
-                nitrogen_source:
-                  - compound: ammonium_sulfate
-                    # Saldanha et al 2004: 5 g/l
-                    concentration_percent: 0.5
-                phosphate_source:
-                  - compound: potassium_phosphate_monobasic
-                    # Hackett et al 2020: 20 mg/l
-                    concentration_percent: 0.002
-            N:
-              media:
-                nitrogen_source:
-                  - compound: ammonium_sulfate
-                    # Hackett et al 2020: 40 mg/l
-                    concentration_percent: 0.004
-            M:
-              description: "Not defined in the paper or on the Calico website"
-        - name: date
-          dtype: string
-          description: date performed
-          role: experimental_condition
-        - name: strain
-          dtype: string
-          description: strain name
-          role: experimental_condition
-        - name: green_median
-          dtype: float
-          description: median of green (reference) channel fluorescence
-          role: quantitative_measure
-        - name: red_median
-          dtype: float
-          description: median of red (experimental) channel fluorescence
-          role: quantitative_measure
-        - name: log2_ratio
-          dtype: float
-          description: log2(red / green) subtracting value at time zero
-          role: quantitative_measure
-        - name: log2_cleaned_ratio
-          dtype: float
-          description: Non-specific stress response and prominent outliers removed
-          role: quantitative_measure
-        - name: log2_noise_model
-          dtype: float
-          description: estimated noise standard deviation
-          role: quantitative_measure
-        - name: log2_cleaned_ratio_zth2d
-          dtype: float
-          description: >-
-            cleaned timecourses hard-thresholded based on
-            multiple observations (or last observation) passing the noise model
-          role: quantitative_measure
-        - name: log2_selected_timecourses
-          dtype: float
-          description: >-
-            cleaned timecourses hard-thresholded based on single observations
-            passing noise model and impulse evaluation of biological feasibility
-          role: quantitative_measure
-        - name: log2_shrunken_timecourses
-          dtype: float
-          description: >-
-            selected timecourses with observation-level shrinkage based on
-            local FDR (false discovery rate). Most users of the data will want
-            to use this column.
-          role: quantitative_measure
-        - name: responsive
-          dtype: bool
-          description: >-
-            This labels targets, for a given regulator, with abs(log2_shrunken_timecourses) `>` 0
 ---
 # Hackett 2020
 
@@ -318,85 +245,72 @@ transcriptome-wide time series. Mol Syst Biol. 2020 Mar;16(3):e9174. doi:
 10.15252/msb.20199174. PMID: 32181581; PMCID:
 PMC7076914.](https://doi.org/10.15252/msb.20199174)
 
-This repo provides 1 dataset:
-
-- **hackett_2020**: TF overexpression data from Hackett 2020.
-
-## Usage
-
-The python package `tfbpapi` provides an interface to this data which eases
-examining the datasets, field definitions and other operations. You may also 
-download the parquet datasets directly from hugging face by clicking on
-"Files and Versions", or by using the huggingface_cli and duckdb directly.
-In both cases, this provides a method of retrieving dataset and field definitions.
+## Accessing Data
 
-### `tfbpapi`
+The examples below require
+[labretriever](https://github.com/cmatKhan/labretriever#installation)
+(`pip install labretriever`) and/or the
+[HuggingFace Hub client](https://huggingface.co/docs/huggingface_hub/installation)
+(`pip install huggingface_hub`).
 
-After [installing
-tfbpapi](https://github.com/BrentLab/tfbpapi/?tab=readme-ov-file#installation), you can
-adapt this [tutorial](https://brentlab.github.io/tfbpapi/tutorials/hfqueryapi_tutorial/)
-in order to explore the contents of this repository.
+### Accessing Data with labretriever
 
-### huggingface_cli/duckdb
-
-You can retrieves and displays the file paths for each configuration of
-the "BrentLab/hackett_2020" dataset from Hugging Face Hub.
+This repository is part of a collection configured as a unified database using
+[labretriever.VirtualDB](https://cmatkhan.github.io/labretriever/virtual_db_configuration/).
+Download the
+[collection config](https://github.com/BrentLab/tfbpshiny/blob/main/tfbpshiny/brentlab_yeast_collection.yaml)
+and use it to query the data directly in Python, or with an AI assistant using the
+[labretriever plugin](https://cmatkhan.github.io/labretriever/mcp_server/#quick-install-claude-code-plugin).
 
 ```python
-from huggingface_hub import ModelCard
-from pprint import pprint
-
-card = ModelCard.load("BrentLab/hackett_2020", repo_type="dataset")
+from labretriever.virtual_db import VirtualDB
+from labretriever.datacard import DataCard
 
-# cast to dict
-card_dict = card.data.to_dict()
+# Citation and metadata
+card = DataCard("BrentLab/hackett_2020")
+print([c.config_name for c in card.configs])  # list available datasets
+info = card.info()
+print(info["doi"])
+print(info["citation"])
 
-# Get partition information
-dataset_paths_dict = {d.get("config_name"): d.get("data_files")[0].get("path") for d in card_dict.get("configs")}
+# path to the downloaded brentlab_yeast_collection.yaml
+vdb = VirtualDB("/path/to/brentlab_yeast_collection.yaml")
 
-pprint(dataset_paths_dict)
+print(vdb.get_dataset_description("hackett"))
+vdb.query("SELECT * FROM hackett LIMIT 5")
 ```
 
-If you wish to pull the entire repo, due to its size you may need to use an
-[authentication token](https://huggingface.co/docs/hub/en/security-tokens).
-If you do not have one, try omitting the token related code below and see if
-it works. Else, create a token and provide it like so:
+### Direct parquet access
+
+The repository contains more data than what is exposed through the collection
+configuration. Use `DataCard.info()` to inspect available files, then download
+and query with DuckDB.
+
+Most files in this repository are single parquet files and can be read directly:
 
 ```python
 from huggingface_hub import snapshot_download
 import duckdb
-import os
 
-repo_id = "BrentLab/hackett_2020"
-
-hf_token = os.getenv("HF_TOKEN")
-
-# Download entire repo to local directory
 repo_path = snapshot_download(
-    repo_id=repo_id,
+    repo_id="BrentLab/hackett_2020",
     repo_type="dataset",
-    token=hf_token
+    allow_patterns="hackett_2020.parquet",
 )
-
-print(f"\n✓ Repository downloaded to: {repo_path}")
-
-# Construct path to the hackett_2020 parquet file
-parquet_path = os.path.join(repo_path, "hackett_2020.parquet")
-print(f"✓ Parquet file at: {parquet_path}")
+conn = duckdb.connect()
+# returns a pandas DataFrame with the first 5 rows
+conn.execute(
+    "SELECT * FROM read_parquet(?) LIMIT 5",
+    [f"{repo_path}/hackett_2020.parquet"],
+).df()
 ```
 
-Use your favorite method of interacting with `parquet` files (eg duckDB, but you could
-use dplyr in R or pandas, too).
+### Accessing using R
 
-```python
-# Connect to DuckDB and query the parquet file
-conn = duckdb.connect()
+Clone the repository and read parquet files directly with
+[arrow](https://arrow.apache.org/docs/r/):
 
-query = """
-SELECT DISTINCT time, mechanism, restriction, date
-FROM read_parquet(?)
-WHERE regulator_symbol = 'ACA1'
-"""
-result = conn.execute(query, [parquet_path]).df()
-print(f"Found {result}")
+```r
+# install.packages("arrow")
+arrow::read_parquet("hackett_2020.parquet")
 ```

hackett_2020.parquet.md5

@@ -1 +0,0 @@
-f9b54be34c55efc1af32cf86c4ca368d  hackett_2020.parquet

hackett_2020_analysis_set.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1bf008a5e5c5d880c9f2eca127bfa4b14390df865b35469ec3f8b00ce58f1a5f
+size 403003879

scripts/adding_analysis_set.R

@@ -0,0 +1,65 @@
+library(arrow)
+library(duckdb)
+library(tidyverse)
+
+
+full_data = arrow::read_parquet("~/code/hf/hackett_2020/hackett_2020.parquet")
+
+con <- duckdb::dbConnect(duckdb::duckdb())
+duckdb::duckdb_register_arrow(con, "hackett_meta", arrow::open_dataset("~/code/hf/hackett_2020/hackett_2020.parquet"))
+
+query <- "
+WITH regulator_tiers AS (
+    SELECT
+        regulator_locus_tag,
+        CASE
+            WHEN BOOL_OR(mechanism = 'ZEV' AND restriction = 'P') THEN 1
+            WHEN BOOL_OR(mechanism = 'GEV' AND restriction = 'P') THEN 2
+            ELSE 3
+        END AS tier
+    FROM hackett_meta
+    GROUP BY regulator_locus_tag
+),
+tier_filtered AS (
+    SELECT
+        h.*,
+        t.tier
+    FROM hackett_meta h
+    JOIN regulator_tiers t USING (regulator_locus_tag)
+    WHERE
+        (t.tier = 1 AND h.mechanism = 'ZEV' AND h.restriction = 'P')
+        OR (t.tier = 2 AND h.mechanism = 'GEV' AND h.restriction = 'P')
+        OR (t.tier = 3 AND h.mechanism = 'GEV' AND h.restriction = 'M')
+)
+SELECT DISTINCT
+    sample_id,
+    db_id,
+    regulator_locus_tag,
+    regulator_symbol,
+    target_locus_tag,
+    target_symbol,
+    time,
+    mechanism,
+    restriction,
+    date,
+    strain,
+    green_median,
+    red_median,
+    log2_ratio,
+    log2_cleaned_ratio,
+    log2_noise_model,
+    log2_cleaned_ratio_zth2d,
+    log2_selected_timecourses,
+    log2_shrunken_timecourses,
+    responsive
+FROM tier_filtered
+WHERE regulator_symbol NOT IN ('GCN4', 'RDS2', 'SWI1', 'MAC1')
+"
+
+result <- DBI::dbGetQuery(con, query)
+duckdb::dbDisconnect(con)
+
+analysis_set_ids <- result |> distinct(sample_id) |> pull(sample_id)
+
+full_data <- full_data |>
+    mutate(analysis_set = sample_id %in% analysis_set_ids)