Replace zip archives with single files; update dataset card

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README.md

@@ -1,3 +1,53 @@
----
-license: mit
----
+---
+license: mit
+---
+
+# PiperNET data
+
+Data for PiperNET, a multi-*omics* platform for elucidating the biosynthetic origin of plant specialized metabolites.
+It holds LC-MS metabolomics and RNA-Seq transcriptomics data from several *Piper* species and tissues, with biological replicates.
+Code and pipeline: [github.com/titodamiani/PiperNET](https://github.com/titodamiani/PiperNET).
+
+## Download
+With the [`hf` command line tool](https://huggingface.co/docs/huggingface_hub/guides/cli):
+```bash
+hf download titodamiani/PiperNET --repo-type dataset --local-dir data
+```
+To download one folder only, add `--include`, for example `--include "processed/*"`.
+To run the code on this data, follow the installation steps in the [code repository](https://github.com/titodamiani/PiperNET).
+
+## Structure
+```
+data/
+├── README.md                        # this dataset card
+├── raw/
+│   ├── lcms/
+│   │   ├── datafiles/               # LC-MS raw files, mzML (140 files)
+│   │   └── metadata.tsv             # sample metadata, read by MZmine
+│   └── rnaseq/piperNN/              # transXpress output, one folder per sample ID (13)
+│       ├── transcriptome.fasta      # de novo assembly
+│       ├── transcriptome.pep        # predicted proteins
+│       ├── transcriptome_expression_isoform.tsv
+│       ├── busco_report.txt
+│       └── annotations/             # Pfam, BLASTp, SignalP, TargetP, TMHMM
+├── interim/
+│   ├── lcms_mzmine/                 # MZmine output: feature table, MS/MS spectra (.mgf), annotations, networks (.graphml)
+│   └── rnaseq_clstr/piperNN/        # CD-HIT clustered proteomes
+├── external/
+│   ├── gnps2/                       # GNPS2 feature-based molecular networking results
+│   ├── sirius/                      # SIRIUS results: CSI:FingerID structures, CANOPUS classes
+│   ├── orthogroups/sonicpd/         # SonicParanoid orthogroups
+│   ├── speclibs/                    # MS/MS spectral libraries for annotation in MZmine
+│   ├── known_enzymes/               # known enzymes table
+│   ├── customDB.csv                 # manually curated list of known LC-MS features, for targeted feature detection in MZmine
+│   ├── standardDB.csv               # read by MZmine and the LC-MS data preparation
+│   └── novelty_scores.csv           # preliminary
+└── processed/
+    ├── ftable_clean.csv             # LC-MS feature table
+    ├── ntable_clean.csv             # GNPS2 node table, for Cytoscape
+    ├── proteomes/piperNN/           # proteome.pep, proteome.csv, blastDB/
+    ├── proteomes_all.csv            # all proteomes with orthogroups
+    └── scoring/                     # input arrays for network-orthogroup scoring (.npy)
+```
+
+`scripts/README.md` in the [code repository](https://github.com/titodamiani/PiperNET) describes how each file is made.

external/customDB.csv

@@ -0,0 +1,42 @@
+mz,rt,adduct,name,formula,neutral_mass,CAS,PubChemCID,smiles,branch,confirmed_std,standard,fragments,samples,FeatID,USI,GNPSdash,comment
+216.138,9.4,[M+H]+,Cinnamoylpiperidine,C14H17NO,215.131,,764160,O=C(N1CCCCC1)/C=C/C2=CC=CC=C2,PL,TRUE,PA03,,"P26, P55",6003,,,
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+274.143,9.66,[M+H]+,Piperlonguminine,C16H19NO3,273.1364,,5320621,CC(CNC(/C=C/C=C/C1=CC2=C(OCO2)C=C1)=O)C,Piperlonguminine,TRUE,PA20,,"P27, P32, P55, P56",6375,,,
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+302.175,10.68,[M+H]+,PubChem-10638035,C18H23NO3,301.1677,,10638035,O=C(/C=C/CCCCC1=CC2=C(OCO2)C=C1)N3CCCC3,Piperyline,,,,"P26, P32, P54,P55",,,,
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external/gnps2/fbmn/flow_filelinking.yaml

@@ -0,0 +1,144 @@
+- parameter: inputfeatures
+  target: inputfeatures/fbmn_quant.csv
+- parameter: inputspectra
+  target: inputspectra/fbmn.mgf
+- parameter: metadata_filename
+  target: metadata_filename/fbmn_metadata.tsv
+- parameter: input_libraries
+  target: input_libraries/MMV_POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-NATURALPRODUCTSLIBRARY_ROUND2_NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-COLLECTIONS-PESTICIDES-POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/BMDMS-NP.mgf
+- parameter: input_libraries
+  target: input_libraries/MSNLIB-POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/LEAFBOT.mgf
+- parameter: input_libraries
+  target: input_libraries/BIRMINGHAM-UHPLC-MS-NEG.mgf
+- parameter: input_libraries
+  target: input_libraries/DEREPLICATOR_IDENTIFIED_LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-NATURALPRODUCTSLIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/RESPECT.mgf
+- parameter: input_libraries
+  target: input_libraries/WFSR-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/MIADB.mgf
+- parameter: input_libraries
+  target: input_libraries/NEO-MSMS.mgf
+- parameter: input_libraries
+  target: input_libraries/HCE-CELL-LYSATE-LIPIDS.mgf
+- parameter: input_libraries
+  target: input_libraries/CASMI.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-COLLECTIONS-PESTICIDES-NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/MSNLIB-NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/PSU-MSMLS.mgf
+- parameter: input_libraries
+  target: input_libraries/IQAMDB.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-SELLECKCHEM-FDA-PART1.mgf
+- parameter: input_libraries
+  target: input_libraries/XANTHONES-DB.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-D2-AMINO-LIPID-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/HMDB.mgf
+- parameter: input_libraries
+  target: input_libraries/BIRMINGHAM-UHPLC-MS-POS.mgf
+- parameter: input_libraries
+  target: input_libraries/MMV_NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-NATURALPRODUCTSLIBRARY_ROUND2_POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/DRUGS-OF-ABUSE-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/MASSBANK.mgf
+- parameter: input_libraries
+  target: input_libraries/BILELIB19.mgf
+- parameter: input_libraries
+  target: input_libraries/AASDB.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-IOBA-NHC.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-MSMLS.mgf
+- parameter: input_libraries
+  target: input_libraries/MCE-DRUG.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-EMBL-MCF.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-CLINICALCOLLECTION2.mgf
+- parameter: input_libraries
+  target: input_libraries/PYRROLIZIDINE-ALKALOID-SPECTRAL-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/ECG-ACYL-AMIDES-C4-C24-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/CMMC-FOOD-BIOMARKERS.mgf
+- parameter: input_libraries
+  target: input_libraries/MONA.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NUTRI-METAB-FEM-POS.mgf
+- parameter: input_libraries
+  target: input_libraries/ECRFS_DB.mgf
+- parameter: input_libraries
+  target: input_libraries/WINE-DB-ORBITRAP.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-SAM-SIK-KANG-LEGACY-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/PNNL-LIPIDS-POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-CLINICALCOLLECTION1.mgf
+- parameter: input_libraries
+  target: input_libraries/UM-NPDC.mgf
+- parameter: input_libraries
+  target: input_libraries/LDB_POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/MASSBANKEU.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-N-ACYL-LIPIDS-MASSQL.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-SELLECKCHEM-FDA-PART2.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-COLLECTIONS-MISC.mgf
+- parameter: input_libraries
+  target: input_libraries/ECG-ACYL-ESTERS-C4-C24-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/DMIM-DRUG-METABOLITE-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIST14-MATCHES.mgf
+- parameter: input_libraries
+  target: input_libraries/PNNL-LIPIDS-NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-FAULKNERLEGACY.mgf
+- parameter: input_libraries
+  target: input_libraries/PHENOLICSDB.mgf
+- parameter: input_libraries
+  target: input_libraries/WINE-DB-QTOF.mgf
+- parameter: input_libraries
+  target: input_libraries/3-HYDROXY-ACYL-AMIDES-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-PRESTWICKPHYTOCHEM.mgf
+- parameter: input_libraries
+  target: input_libraries/BERKELEY-LAB.mgf
+- parameter: input_libraries
+  target: input_libraries/SUMNER.mgf
+- parameter: input_libraries
+  target: input_libraries/ELIXDB-LICHEN-DATABASE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-SMALLMOLECULEPHARMACOLOGICALLYACTIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/LDB_NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NUTRI-METAB-FEM-NEG.mgf
+- parameter: input_libraries
+  target: input_libraries/TUEBINGEN-NATURAL-PRODUCT-COLLECTION.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-SCIEX-LIBRARY.mgf

external/gnps2/fbmn/job_dag.html

@@ -0,0 +1,109 @@
+<!--
+  ~ Copyright 2013-2024, Seqera Labs
+  ~
+  ~ Licensed under the Apache License, Version 2.0 (the "License");
+  ~ you may not use this file except in compliance with the License.
+  ~ You may obtain a copy of the License at
+  ~
+  ~     http://www.apache.org/licenses/LICENSE-2.0
+  ~
+  ~ Unless required by applicable law or agreed to in writing, software
+  ~ distributed under the License is distributed on an "AS IS" BASIS,
+  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  ~ See the License for the specific language governing permissions and
+  ~ limitations under the License.
+  -->
+<html>
+<head>
+<meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
+</head>
+<body>
+<pre class="mermaid" style="text-align: center;">
+flowchart TB
+    subgraph " "
+    v0["Channel.fromPath"]
+    v1["ready"]
+    v4["Channel.fromPath"]
+    v5["Channel.fromPath"]
+    v10["Channel.fromPath"]
+    v25["Channel.fromPath"]
+    v30["Channel.fromPath"]
+    end
+    v2([filesummary])
+    subgraph " "
+    v3[" "]
+    v7["_embedded_metadata_ch"]
+    v9["_spectra_reformatted_ch2"]
+    v32[" "]
+    v33[" "]
+    v35[" "]
+    end
+    v6([quantification_table_reformatted])
+    v8([filter_spectra])
+    v11([librarySearchData])
+    v13([librarymergeResults])
+    v15([summaryLibrary])
+    v18([librarygetGNPSAnnotations])
+    v20([networkingGNPSPrepParams])
+    v22([calculatePairs])
+    v24([filterNetwork])
+    v27([createMetadataFile])
+    v28([calculateGroupings])
+    v29([enrichClusterSummary])
+    v31([createNetworkGraphML])
+    v34([createTallRawData])
+    v12(( ))
+    v14(( ))
+    v16(( ))
+    v19(( ))
+    v21(( ))
+    v23(( ))
+    v26(( ))
+    v0 --> v2
+    v0 --> v34
+    v1 --> v2
+    v2 --> v3
+    v4 --> v6
+    v5 --> v6
+    v6 --> v8
+    v6 --> v7
+    v6 --> v28
+    v6 --> v34
+    v8 --> v9
+    v8 --> v11
+    v8 --> v20
+    v8 --> v22
+    v10 --> v11
+    v10 --> v15
+    v11 --> v12
+    v12 --> v13
+    v13 --> v14
+    v15 --> v16
+    v14 --> v18
+    v16 --> v18
+    v18 --> v19
+    v20 --> v21
+    v21 --> v22
+    v22 --> v23
+    v23 --> v24
+    v24 --> v29
+    v24 --> v31
+    v25 --> v26
+    v26 --> v27
+    v27 --> v28
+    v28 --> v29
+    v19 --> v29
+    v29 --> v31
+    v30 --> v31
+    v19 --> v31
+    v31 --> v33
+    v31 --> v32
+    v34 --> v35
+
+</pre>
+<script type="module">
+  import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs';
+  mermaid.initialize({ startOnLoad: true });
+</script>
+</body>
+</html>

external/gnps2/fbmn/job_parameters.yaml

@@ -0,0 +1,33 @@
+OMETAFLOW_SERVER: http://ometaflow-launchserver:4000
+OMETALIBRARY_SERVER: http://ometalibrary-web:5000/library
+OMETAMASST_SERVER: http://ometamasst-web:5000/masst
+OMETATASK: 16b6a354fd68486e9638497b8e105437
+OMETAUSER: Tito_Damiani
+create_time: 2025-07-13 23:18:51 PDT-0700
+description: 20250714_PiperNET_fbmn
+featurefindingtool: MZMINE
+fragment_tolerance: '0.01'
+input_libraries: /data/nf_data/server/nf_tasks/16b6a354fd68486e9638497b8e105437/input_libraries
+input_raw_spectra: NO_FILE
+input_supplemental_edges: NO_FILE
+inputfeatures: /data/nf_data/server/nf_tasks/16b6a354fd68486e9638497b8e105437/inputfeatures/fbmn_quant.csv
+inputspectra: /data/nf_data/server/nf_tasks/16b6a354fd68486e9638497b8e105437/inputspectra
+library_analog_max_shift: '1999'
+library_analog_search: '1'
+library_min_cosine: '0.7'
+library_min_matched_peaks: '6'
+library_topk: '1'
+metadata_filename: /data/nf_data/server/nf_tasks/16b6a354fd68486e9638497b8e105437/metadata_filename/fbmn_metadata.tsv
+networking_max_shift: '1999'
+networking_min_cosine: '0.7'
+networking_min_matched_peaks: '6'
+normalization: None
+pm_tolerance: '0.01'
+precursor_filter: '1'
+publishdir: /data/nf_data/server/nf_tasks/16b6a354fd68486e9638497b8e105437
+task: 16b6a354fd68486e9638497b8e105437
+topology_maxcomponent: '100'
+topology_topk: '10'
+window_filter: '1'
+workflow_version: SERVER:2025.06.17;WORKFLOW:2025.07.09
+workflowname: feature_based_molecular_networking_workflow

external/gnps2/fbmn/nf_cmd.sh

@@ -0,0 +1 @@
+nextflow run /app/workflows_user/feature_based_molecular_networking_workflow/nf_workflow.nf -params-file /data/nf_data/server/nf_tasks/16b6a354fd68486e9638497b8e105437/job_parameters.yaml -w /data/nf_data/server/nf_work/16b6a354fd68486e9638497b8e105437 -with-report /data/nf_data/server/nf_tasks/16b6a354fd68486e9638497b8e105437/job_report.html -with-timeline /data/nf_data/server/nf_tasks/16b6a354fd68486e9638497b8e105437/job_timeline.html -with-dag /data/nf_data/server/nf_tasks/16b6a354fd68486e9638497b8e105437/job_dag.html -with-weblog http://localhost:4000/nf_weblog/16b6a354fd68486e9638497b8e105437 -c /app/launchserver/nextflow.config

external/gnps2/fbmn/nf_output/3-HYDROXY-ACYL-AMIDES-LIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/AASDB.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/BERKELEY-LAB.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/BILELIB19.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/BIRMINGHAM-UHPLC-MS-NEG.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/BIRMINGHAM-UHPLC-MS-POS.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/BMDMS-NP.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/CASMI.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/CMMC-FOOD-BIOMARKERS.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/DEREPLICATOR_IDENTIFIED_LIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/DMIM-DRUG-METABOLITE-LIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/DRUGS-OF-ABUSE-LIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/ECG-ACYL-AMIDES-C4-C24-LIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/ECG-ACYL-ESTERS-C4-C24-LIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/ECRFS_DB.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/ELIXDB-LICHEN-DATABASE.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-COLLECTIONS-MISC.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-COLLECTIONS-PESTICIDES-NEGATIVE.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-COLLECTIONS-PESTICIDES-POSITIVE.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-D2-AMINO-LIPID-LIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-EMBL-MCF.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-FAULKNERLEGACY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-IOBA-NHC.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-LIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-MSMLS.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-N-ACYL-LIPIDS-MASSQL.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-NIH-CLINICALCOLLECTION1.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-NIH-CLINICALCOLLECTION2.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-NIH-NATURALPRODUCTSLIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-NIH-NATURALPRODUCTSLIBRARY_ROUND2_NEGATIVE.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-NIH-NATURALPRODUCTSLIBRARY_ROUND2_POSITIVE.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-NIH-SMALLMOLECULEPHARMACOLOGICALLYACTIVE.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-NIST14-MATCHES.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-NUTRI-METAB-FEM-NEG.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-NUTRI-METAB-FEM-POS.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-PRESTWICKPHYTOCHEM.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-SAM-SIK-KANG-LEGACY-LIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-SCIEX-LIBRARY.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-SELLECKCHEM-FDA-PART1.mgf.tsv

@@ -0,0 +1 @@
+

external/gnps2/fbmn/nf_output/GNPS-SELLECKCHEM-FDA-PART2.mgf.tsv

@@ -0,0 +1 @@
+