cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/1fb-3b4-063
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/270-nvw-ky7
title: Ranunculus chius DC.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/hcw-z0s-cmj
title: Ranunculus peltatus Schrank

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/3t8-aw5-edv
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/sb1-xbk-pfr
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/8qm-hfn-4vm
title: Ranunculus peltatus Schrank

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/9my-hdc-fmy
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/38j-zyh-p5x
title: Prunus spinosa L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/214-mzh-np5
title: Prunus spinosa L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/has-5aq-4yp
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/0f6-bnb-7gk
title: Prunus spinosa L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/1ng-7e1-0vp
title: Pulmonaria officinalis L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/107-pq6-pah
title: Pulmonaria mollis Wulfen ex Hornem.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/s8s-fft-r11
title: Pulmonaria mollis Wulfen ex Hornem.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/xa0-e6y-7av
title: Prunus cerasifera Ehrh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/1dm-657-yg1
title: Prunus domestica L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/kzg-9cs-j70
title: Prunus domestica L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/aj3-6zr-way
title: Ranunculus arvensis L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/eak-0tx-s0g
title: Ranunculus marginatus d'Urv.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/azf-2jj-02f
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/4z5-0nn-rzj
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/7n2-rnf-dq1
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/7lm-ec5-ja6
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/pst-68j-az9
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/d57-7nn-11f
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/ez5-wyq-b7v
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/1l5-wf3-948
title: Ptilostemon stellatus (L.) Greuter

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/ej7-6js-tt3
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/cy2-vry-h0x
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/ddp-nhj-0nt
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/f6r-x9g-zyt
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/wrh-g0y-4dk
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/0gn-nas-4t4
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/f0l-rez-hr4
title: Quercus frainetto Ten.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/m1w-3g9-74h
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/fdl-7zp-2z5
title: Ranunculus arvensis L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/t64-sq8-p07
title: Quercus frainetto Ten.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/njj-pfc-zgc
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/hmd-z9s-7kz
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/xqh-ysg-g28
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/6yj-lrn-q1h
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/pzc-80l-jdj
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/bqm-6dl-ayf
title: Quercus frainetto Ten.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/mnx-fwv-f4y
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/rfq-7af-431
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/96r-wkn-wga
title: Pulicaria dysenterica (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/dq3-ahd-80n
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/8e6-rd2-sfy
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/jmm-9v8-bxw
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.5883/ds-epernsp
title: PETER HUEMER, TONI MAYR, JACQUES NEL and WOLFGANG STARK

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.3535/987-176-6ls
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/p4p-3rc-5t8
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/3yn-1j8-f6c
title: Quercus frainetto Ten.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/36c-w9v-m63
title: Quercus frainetto Ten.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/nmj-k76-8rc
title: Quercus frainetto Ten.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/alb-dad-jme
title: Quercus frainetto Ten.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/pyx-81x-bed
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/a4y-3sb-efw
title: Ranunculus gracilis E. D. Clarke

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/jlq-nhy-0bx
title: Prunus lusitanica L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/xkk-611-478
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/h9w-5bt-5q7
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/r55-yg7-xym
title: Punica granatum L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/dg9-16a-ypp
title: Prunus mahaleb L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/f1z-13x-awt
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/1zl-5az-q74
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/qvy-jsz-b3m
title: Prunus avium (L.) L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/pql-dbb-445
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/3eg-qaa-5mt
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/lys-q99-5ag
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/04x-edr-2dm
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/7k8-zpd-4t7
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/aky-ze0-pkt
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/2s7-29a-xn0
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/shz-nf0-8ed
title: Ranunculus trichophyllus Chaix

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/dma-fq3-kla
title: Prunus dulcis (Mill.) D. A. Webb

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/eft-rvc-c9g
title: Prunus dulcis (Mill.) D. A. Webb

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/20m-kdj-5gt
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/e8k-gzp-sc3
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/b30-0ec-g42
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/hcm-mhw-8xd
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/ez8-366-6xl
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/k0l-jg4-9ls
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/blz-27h-737
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/2bc-9db-bfk
title: Bituminaria bituminosa (L.) C.H.Stirt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/kc5-ywn-s33
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/6am-1p0-jav
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/nvs-0wz-whw
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/8by-p98-l1z
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/aq3-x89-z8n
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/0nl-2ap-cz8
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/g9s-kqy-qlq
title: Ficaria verna subsp. verna

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.5281/zenodo.15300194
title: UK Authors - 2022 Dataset

description: This dataset contains the raw, anonymised data that was collected to produce the report UK Authors' Earnings and Contracts: A Survey of 60.000 writers. It includes responses from UK-based authors, covering earnings, contracts, demographics, and working conditions.
DOI: 10.5281/zenodo.15300195
title: UK Authors - 2022 Dataset

description: This dataset contains the raw, anonymised data that was collected to produce the report UK Authors' Earnings and Contracts: A Survey of 60.000 writers. It includes responses from UK-based authors, covering earnings, contracts, demographics, and working conditions.
DOI: 10.15468/dl.nv855y
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sus scrofa",
 "Country is Saint Lucia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025261-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yz7s2d
title: Occurrence Download

description: A dataset containing 1364 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sus scrofa",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1364 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025260-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uyaq3y
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sus scrofa",
 "Country is Saint Kitts and Nevis",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025262-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16284913
title: MGMG: Cell Morphology-Guided Molecule Generation for Drug Discovery

description: This dataset supports MGMG (Morphology-Guided Molecule Generation), a phenotypic drug discovery-oriented framework that integrates morphological information from compound treatment with molecular textual descriptions to enable de novo molecule design without the need for target information. Please cite this publication when using the dataset:





MGMG: Cell Morphology-Guided Molecule Generation for Drug Discovery


Qiaosi Tang, Daoyun Ding, Xiaoyong Yuan, Gustavo Seabra, Peter A Ramdhan, Chi-Yuan Liu, My T. Thai, Chenglong Li, Hendrik Luesch, Yanjun Li

bioRxiv 2025.07.11.664424; doi: https://doi.org/10.1101/2025.07.11.664424


Overview

The dataset contains model checkpoint, input test data, and results required to reproduce MGMG’s evaluations and case studies, including the activator design task and docking task. It is structured to support reproducibility, downstream applications, and benchmarking by the research community. All data is organized under the archive file MGMG_dataset.zip.

Contents

checkpoint/





pytorch_model.bin: Saved checkpoint of the trained MGMG model.



testset_Morphology-BBBC036v1/





unique_morph_info.json: Morphological profiles for the test compounds, derived from Cell Painting images in BBBC036v1 (Bray et al. 2017) and processed using PyCytominer.



testset_Mol-Instructions-BBBC036v1/





task3_MolIns_text2mol_test_tk.json: Compound textual descriptions sourced from PubChem, aligned with the same compounds in the morphology set.



testset_MolCaptioned-BBBC036v1/





task3_MolIns_text2mol_test_tkgendesc_revised.json: Synthetic compound textual descriptions generated by BioT5, aligned with the same compounds in the morphology set.



reference_metrics/





test_gth.csv: Test set reference compound chemical properties.


train_gth.csv: Train set reference compound chemical properties.


activator_design/





task3_GeneOE_text2mol_test_[GENE].json: Textual descriptions for gene-specific molecule generation inputs, where each file corresponds to a gene overexpression case (e.g., TP53, BRCA1, NFKB1), with text profiles generated by GPT-4.0. Used for the first step of the activator design task (See the preprint Methods section for more details).




task3_GeneOEbiot5gen_test.json: BioT5-generated molecular descriptions for all gene perturbation cases. Used for the third step of the activator design task (See the preprint Methods section for more details).




unique_gene_morph_info.json: Morphological profiles of cells with gene overexpression perturbations, used for the activator design case study in the manuscript.



docking_files/





[PDB_ID].maegz: Prepared docking files (protein target, reference and generated sample compounds) for select demo cases (3CMF, 4E2J, 7DFP, 7QZ7), compatible with Maestro/PyMOL.
DOI: 10.5281/zenodo.16296425
title: MGMG: Cell Morphology-Guided Molecule Generation for Drug Discovery

description: This dataset supports MGMG (Morphology-Guided Molecule Generation), a phenotypic drug discovery-oriented framework that integrates morphological information from compound treatment with molecular textual descriptions to enable de novo molecule design without the need for target information. Please cite this publication when using the dataset:





MGMG: Cell Morphology-Guided Molecule Generation for Drug Discovery


Qiaosi Tang, Daoyun Ding, Xiaoyong Yuan, Gustavo Seabra, Peter A Ramdhan, Chi-Yuan Liu, My T. Thai, Chenglong Li, Hendrik Luesch, Yanjun Li

bioRxiv 2025.07.11.664424; doi: https://doi.org/10.1101/2025.07.11.664424


Overview

The dataset contains model checkpoint, input test data, and results required to reproduce MGMG’s evaluations and case studies, including the activator design task and docking task. It is structured to support reproducibility, downstream applications, and benchmarking by the research community. All data is organized under the archive file MGMG_dataset.zip.

Contents

checkpoint/





pytorch_model.bin: Saved checkpoint of the trained MGMG model.



testset_Morphology-BBBC036v1/





unique_morph_info.json: Morphological profiles for the test compounds, derived from Cell Painting images in BBBC036v1 (Bray et al. 2017) and processed using PyCytominer.



testset_Mol-Instructions-BBBC036v1/





task3_MolIns_text2mol_test_tk.json: Compound textual descriptions sourced from PubChem, aligned with the same compounds in the morphology set.



testset_MolCaptioned-BBBC036v1/





task3_MolIns_text2mol_test_tkgendesc_revised.json: Synthetic compound textual descriptions generated by BioT5, aligned with the same compounds in the morphology set.



reference_metrics/





test_gth.csv: Test set reference compound chemical properties.


train_gth.csv: Train set reference compound chemical properties.


activator_design/





task3_GeneOE_text2mol_test_[GENE].json: Textual descriptions for gene-specific molecule generation inputs, where each file corresponds to a gene overexpression case (e.g., TP53, BRCA1, NFKB1), with text profiles generated by GPT-4.0. Used for the first step of the activator design task (See the preprint Methods section for more details).




task3_GeneOEbiot5gen_test.json: BioT5-generated molecular descriptions for all gene perturbation cases. Used for the third step of the activator design task (See the preprint Methods section for more details).




unique_gene_morph_info.json: Morphological profiles of cells with gene overexpression perturbations, used for the activator design case study in the manuscript.



docking_files/





[PDB_ID].maegz: Prepared docking files (protein target, reference and generated sample compounds) for select demo cases (3CMF, 4E2J, 7DFP, 7QZ7), compatible with Maestro/PyMOL.
DOI: 10.15468/dl.rqsqfh
title: Occurrence Download

description: A dataset containing 2163 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Avena abyssinica"
 ]
}

 The dataset includes 2163 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025263-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.