← All .science files
pmid:26649327
Data in support of the proteomic analysis of plasma membrane and tonoplast from the leaves of mangrove plant Avicennia officinalis.
Pannaga Krishnamurthy · Xing Fei Tan · Teck Kwang Lim · Tit-Meng Lim · Prakash P Kumar · Chiang-Shiong Loh · Qingsong Lin
Data in brief · 2015 doi:10.1016/j.dib.2015.10.016
Paper
complete
Experiment
complete
Data
partial
Analysis
absent
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 7 items
claims array · 2 items
[0] object · 6 fields
[1] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 4 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 9 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 9 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
gaps array · 2 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 4 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 8 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26649327", "kind": "science-record", "revision": 3, "content_hash": "sha256:6267b96950f4ddc91b842696886a319bbaefc23d1f53ed2309868b7e207f7721", "created_at": "2026-11-01T15:40:14Z", "updated_at": "2026-11-01T18:47:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Data in support of the proteomic analysis of plasma membrane and tonoplast from the leaves of mangrove plant Avicennia officinalis.", "doi": "10.1016/j.dib.2015.10.016", "pmid": "26649327", "authors": ["Pannaga Krishnamurthy", "Xing Fei Tan", "Teck Kwang Lim", "Tit-Meng Lim", "Prakash P Kumar", "Chiang-Shiong Loh", "Qingsong Lin"], "journal": "Data in brief", "year": 2015, "abstract": "The data provides information in support of the research article, Proteomics 2014, 14, 2545-2557 [1]. Raw data is available from the ProteomeXchange Consortium via the PRIDE partnerRepository [2] with the dataset identifier PXD000837. Plasma membrane and tonoplast proteins from the leaves of Avicennia officinalis were identified using gel electrophoresis (one and two dimensional) combined with LC-MS analysis. Based on GO annotation, identified proteins were predicted to be involved in various biological processes.", "claims": [{"id": "claim-data-access", "statement": "Raw data is available from the ProteomeXchange Consortium via the PRIDE partnerRepository [2] with the dataset identifier PXD000837.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26649327", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw data is available from the ProteomeXchange Consortium via the PRIDE partnerRepository [2] with the dataset identifier PXD000837."}], "state": "complete"}, {"id": "claim-target-result", "statement": "No numerical result was reported for the registered target; no FDR analysis was performed, and the source data are available through PRIDE under dataset identifier PXD000837.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26649327", "locator": "sections[8] \"LC–MS/MS analysis\" paragraph 2", "quote": "No FDR analysis was performed on the dataset."}, {"asset": "source:pmid:26649327", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw data is available from the ProteomeXchange Consortium via the PRIDE partnerRepository [2] with the dataset identifier PXD000837."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "No numerical result was reported for the registered target; no FDR analysis was performed, and the source data are available through PRIDE under dataset identifier PXD000837.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26649327"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD000837"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD000837"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26649327", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2015.10.016", "sha256": "sha256:d3d039209c69f2583bb8e8bcf0b5c80dc84d607f298ddd80b7ebaa8f8bd6a1d0", "bytes": 13452, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2015.10.016", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4644245", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD000837", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD000837", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000837", "version": null, "note": "Raw data is available from the ProteomeXchange Consortium via the PRIDE partnerRepository [2] with the dataset identifier PXD000837.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw data is available from the ProteomeXchange Consortium via the PRIDE partnerRepository [2] with the dataset identifier PXD000837.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic analysis of plasma membrane and tonoplast from the leaves of a mangrove plant Avicennia officinalis", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26649327:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:92aad9d6bfd48da785ab927cf21d147e2de8102a3aae706c217d2cbebeaf0db0", "bytes": 1180, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4644245", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biology"], ["More specific subject area", "Membrane proteomics and mass spectrometry (MS)"], ["Type of data", "MS data and annotations"], ["How data was acquired", "Mass spectrometry: Data was acquired on the instrument TripleTOF 5600 (SCIEX, Foster City, CA, USA)."], ["Data format", "Raw and processed data"], ["Experimental factors", "Plasma membrane and tonoplast membrane protein fractions were isolated from the leaves of field-growing Avicennia officinalis trees using two-aqueous-phase partitioning and density gradient centrifugation, respectively."], ["Experimental features", "The plasma membrane and tonoplast membrane proteins were fractionated by 1DE and 2DE. The peptides resulting from in-gel tryptic digestion were fractionated and analyzed using LC–MS/MS."], ["Data source location", "Singapore"], ["Data accessibility", "Deposited to the ProteomeXchange Consortium via the PRIDE partnerRepository[2]with the dataset identifier PXD000837 (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000837)"]], "row_count": 9, "column_count": 2, "numeric_cells": 3, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26649327:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:92aad9d6bfd48da785ab927cf21d147e2de8102a3aae706c217d2cbebeaf0db0", "bytes": 1180, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4644245", "section_index": 2, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biology"], ["More specific subject area", "Membrane proteomics and mass spectrometry (MS)"], ["Type of data", "MS data and annotations"], ["How data was acquired", "Mass spectrometry: Data was acquired on the instrument TripleTOF 5600 (SCIEX, Foster City, CA, USA)."], ["Data format", "Raw and processed data"], ["Experimental factors", "Plasma membrane and tonoplast membrane protein fractions were isolated from the leaves of field-growing Avicennia officinalis trees using two-aqueous-phase partitioning and density gradient centrifugation, respectively."], ["Experimental features", "The plasma membrane and tonoplast membrane proteins were fractionated by 1DE and 2DE. The peptides resulting from in-gel tryptic digestion were fractionated and analyzed using LC–MS/MS."], ["Data source location", "Singapore"], ["Data accessibility", "Deposited to the ProteomeXchange Consortium via the PRIDE partnerRepository[2]with the dataset identifier PXD000837 (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000837)"]], "row_count": 9, "column_count": 2, "numeric_cells": 3, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:PXD000837 not downloaded", "asset:data:geo:PXD000837 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD000837"], "resolved_accessions": ["PXD000837"], "statements": ["Raw data is available from the ProteomeXchange Consortium via the PRIDE partnerRepository [2] with the dataset identifier PXD000837."], "basis": "The paper names PXD000837 in ProteomeXchange Consortium via the PRIDE partnerRepository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26649327", "data:geo:PXD000837", "asset:table:pmid:26649327:1", "asset:table:pmid:26649327:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD000837"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:33Z", "independence": "same_provider"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 32533, "completion_tokens": 2960, "cached_tokens": 2088}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:26649327", "type": "paper", "label": "pmid:26649327"}, {"id": "source:pmid:26649327", "type": "manuscript", "label": "PMID 26649327 full text"}, {"id": "data:geo:PXD000837", "type": "dataset", "label": "GEO PXD000837"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26649327", "type": "paper", "label": "pmid:26649327"}, {"id": "source:pmid:26649327", "type": "manuscript", "label": "PMID 26649327 full text"}, {"id": "data:geo:PXD000837", "type": "dataset", "label": "GEO PXD000837"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26649327", "type": "extraction", "used": ["source:pmid:26649327"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD000837", "type": "accession_resolution", "used": ["data:geo:PXD000837"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:26649327", "parent_hash": "sha256:58aa7d055a3fcb38b19f07427ec2d9ffb6fbd1e14df01b30ff21beb2d4b27985", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD000837 licence not read", "asset:data:geo:PXD000837 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"]}