From af575f7d2ab5539cbef305a3e793772b0373c01a Mon Sep 17 00:00:00 2001
From: "Jochens, Florian" <fj@andaco.de>
Date: Wed, 10 Nov 2021 12:31:41 +0100
Subject: [PATCH] example urls
---
input/__pycache__/input_fj.cpython-39.pyc | Bin 0 -> 4300 bytes
input/example_urls | 2 +
input/test.py | 2 +-
input/x | 234 ++++++++++++++++++++++
4 files changed, 237 insertions(+), 1 deletion(-)
create mode 100644 input/__pycache__/input_fj.cpython-39.pyc
create mode 100644 input/example_urls
create mode 100644 input/x
diff --git a/input/__pycache__/input_fj.cpython-39.pyc b/input/__pycache__/input_fj.cpython-39.pyc
new file mode 100644
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diff --git a/input/example_urls b/input/example_urls
new file mode 100644
index 0000000..96ac680
--- /dev/null
+++ b/input/example_urls
@@ -0,0 +1,2 @@
+https://pubs.acs.org/doi/10.1021/acs.jcim.5b00332
+https://pubs.acs.org/doi/10.1021/acs.jcim.6b00709
diff --git a/input/test.py b/input/test.py
index bdd12e8..dc623ca 100755
--- a/input/test.py
+++ b/input/test.py
@@ -4,7 +4,7 @@ from input_fj import input, print_pub_info
import sys
if len(sys.argv) != 3:
- sys.stderr.write('Usage: {} <url>\n'.format(sys.argv[0]))
+ sys.stderr.write('Usage: {} <url> <url>\n'.format(sys.argv[0]))
exit(1)
url = sys.argv[1]
url2 = sys.argv[2]
diff --git a/input/x b/input/x
new file mode 100644
index 0000000..c8ade9d
--- /dev/null
+++ b/input/x
@@ -0,0 +1,234 @@
+Article title: Feasibility of Active Machine Learning for Multiclass Compound Classification
+Publication date: January 7, 2016
+DOI-URL: https://doi.org/10.1021/acs.jcim.5b00332
+
+Subjects:
+Algorithms, Molecules, Drug discovery, Screening assays, Receptors
+
+Contributors:
+Tobias Lang, Florian Flachsenberg, Ulrike von Luxburg, Matthias Rarey
+
+This publication is cited by the following 30 publications:
+
+
+ Title: Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery
+ Journal: Chemical Reviews
+ Contributors: Xin Yang, Yifei Wang, Ryan Byrne, Gisbert Schneider, Shengyong Yang.
+ DOI-URL: https://doi.org/10.1021/acs.chemrev.8b00728
+
+
+ Title: De Novo Molecule Design by Translating from Reduced Graphs to SMILES
+ Journal: Journal of Chemical Information and Modeling
+ Contributors: Peter Pogány, Navot Arad, Sam Genway, Stephen D. Pickett.
+ DOI-URL: https://doi.org/10.1021/acs.jcim.8b00626
+
+
+ Title: Designing Algorithms To Aid Discovery by Chemical Robots
+ Journal: ACS Central Science
+ Contributors: Alon B. Henson, Piotr S. Gromski, Leroy Cronin.
+ DOI-URL: https://doi.org/10.1021/acscentsci.8b00176
+
+
+ Title: Modeling Kinase Inhibition Using Highly Confident Data Sets
+ Journal: Journal of Chemical Information and Modeling
+ Contributors: Sorin Avram, Alina Bora, Liliana Halip, Ramona Curpăn.
+ DOI-URL: https://doi.org/10.1021/acs.jcim.7b00729
+
+
+ Title: Predictive Models for Fast and Effective Profiling of Kinase Inhibitors
+ Journal: Journal of Chemical Information and Modeling
+ Contributors: Alina Bora, Sorin Avram, Ionel Ciucanu, Marius Raica, and Stefana Avram .
+ DOI-URL: https://doi.org/10.1021/acs.jcim.5b00646
+
+
+ Title: Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery
+ Journal: Bioinformatics
+ Contributors: Huangqingbo Sun, Robert F Murphy, .
+ DOI-URL: https://doi.org/10.1093/bioinformatics/btab322
+
+
+ Title: An Artificial Intelligence Approach Based on Hybrid CNN-XGB Model to Achieve High Prediction Accuracy through Feature Extraction, Classification and Regression for Enhancing Drug Discovery in Biomedicine
+ Journal: International Journal of Biology and Biomedical Engineering
+ Contributors: Mukesh Madanan, Biju T. Sayed, Nurul Akhmal Mohd Zulkefli, Nitha C. Velayudhan.
+ DOI-URL: https://doi.org/10.46300/91011.2021.15.22
+
+
+ Title: Artificial Intelligence in Medicinal Chemistry
+ Journal:
+ Contributors: Edward Griffen, Alexander Dossetter, Andrew Leach, Shane Montague.
+ DOI-URL: https://doi.org/10.1002/0471266949.bmc267
+
+
+ Title: Practical Chemogenomic Modeling and Molecule Discovery Strategies Unveiled by Active Learning
+ Journal:
+ Contributors: J.B. Brown.
+ DOI-URL: https://doi.org/10.1016/B978-0-12-801238-3.11533-8
+
+
+ Title: Machine learning phases and criticalities without using real data for training
+ Journal: Physical Review B
+ Contributors: D.-R. Tan, F.-J. Jiang.
+ DOI-URL: https://doi.org/10.1103/PhysRevB.102.224434
+
+
+ Title: Active learning effectively identifies a minimal set of maximally informative and asymptotically performant cytotoxic structure–activity patterns in NCI-60 cell lines
+ Journal: RSC Medicinal Chemistry
+ Contributors: Takumi Nakano, Shunichi Takeda, J.B. Brown.
+ DOI-URL: https://doi.org/10.1039/D0MD00110D
+
+
+ Title: Active learning efficiently converges on rational limits of toxicity prediction and identifies patterns for molecule design
+ Journal: Computational Toxicology
+ Contributors: Ahsan Habib Polash, Takumi Nakano, Christin Rakers, Shunichi Takeda, J.B. Brown.
+ DOI-URL: https://doi.org/10.1016/j.comtox.2020.100129
+
+
+ Title: Practical considerations for active machine learning in drug discovery
+ Journal: Drug Discovery Today: Technologies
+ Contributors: Daniel Reker.
+ DOI-URL: https://doi.org/10.1016/j.ddtec.2020.06.001
+
+
+ Title: Designing compact training sets for data-driven molecular property prediction through optimal exploitation and exploration
+ Journal: Molecular Systems Design & Engineering
+ Contributors: Bowen Li, Srinivas Rangarajan.
+ DOI-URL: https://doi.org/10.1039/C9ME00078J
+
+
+ Title: Applicability Domain of Active Learning in Chemical Probe Identification: Convergence in Learning from Non-Specific Compounds and Decision Rule Clarification
+ Journal: Molecules
+ Contributors: Ahsan Habib Polash, Takumi Nakano, Shunichi Takeda, J.B. Brown.
+ DOI-URL: https://doi.org/10.3390/molecules24152716
+
+
+ Title: Capturing and applying knowledge to guide compound optimisation
+ Journal: Drug Discovery Today
+ Contributors: Matthew Segall, Tamsin Mansley, Peter Hunt, Edmund Champness.
+ DOI-URL: https://doi.org/10.1016/j.drudis.2019.02.004
+
+
+ Title: A novel graph kernel on chemical compound classification
+ Journal: Journal of Bioinformatics and Computational Biology
+ Contributors: Qiangrong Jiang, Jiajia Ma.
+ DOI-URL: https://doi.org/10.1142/S0219720018500269
+
+
+ Title: Accelerating Drug Discovery Using Convolution Neural Network Based Active Learning
+ Journal:
+ Contributors: Pengfei Liu, Kwong-Sak Leung.
+ DOI-URL: https://doi.org/10.1109/TENCON.2018.8650298
+
+
+ Title: An Adaptive Lightweight Security Framework Suited for IoT
+ Journal:
+ Contributors: Menachem Domb.
+ DOI-URL: https://doi.org/10.5772/intechopen.73712
+
+
+ Title: Adaptive mining and model building of medicinal chemistry data with a multi-metric perspective
+ Journal: Future Medicinal Chemistry
+ Contributors: JB Brown.
+ DOI-URL: https://doi.org/10.4155/fmc-2018-0188
+
+
+ Title: Chemogenomic Active Learning's Domain of Applicability on Small, Sparse qHTS Matrices: A Study Using Cytochrome P450 and Nuclear Hormone Receptor Families
+ Journal: ChemMedChem
+ Contributors: Christin Rakers, Rifat Ara Najnin, Ahsan Habib Polash, Shunichi Takeda, J.B. Brown.
+ DOI-URL: https://doi.org/10.1002/cmdc.201700677
+
+
+ Title: Automating drug discovery
+ Journal: Nature Reviews Drug Discovery
+ Contributors: Gisbert Schneider.
+ DOI-URL: https://doi.org/10.1038/nrd.2017.232
+
+
+ Title: Classifiers and their Metrics Quantified
+ Journal: Molecular Informatics
+ Contributors: J. B. Brown.
+ DOI-URL: https://doi.org/10.1002/minf.201700127
+
+
+ Title: Active Search for Computer-aided Drug Design
+ Journal: Molecular Informatics
+ Contributors: Dino Oglic, Steven A. Oatley, Simon J. F. Macdonald, Thomas Mcinally, Roman Garnett, Jonathan D. Hirst, Thomas Gärtner.
+ DOI-URL: https://doi.org/10.1002/minf.201700130
+
+
+ Title: Selection of Informative Examples in Chemogenomic Datasets
+ Journal:
+ Contributors: Daniel Reker, J. B. Brown.
+ DOI-URL: https://doi.org/10.1007/978-1-4939-8639-2_13
+
+
+ Title: The value of prior knowledge in machine learning of complex network systems
+ Journal: Bioinformatics
+ Contributors: Dana Ferranti, David Krane, David Craft, .
+ DOI-URL: https://doi.org/10.1093/bioinformatics/btx438
+
+
+ Title: Lightweight adaptive Random-Forest for IoT rule generation and execution
+ Journal: Journal of Information Security and Applications
+ Contributors: Menachem Domb, Elisheva Bonchek-Dokow, Guy Leshem.
+ DOI-URL: https://doi.org/10.1016/j.jisa.2017.03.001
+
+
+ Title: Active learning for computational chemogenomics
+ Journal: Future Medicinal Chemistry
+ Contributors: Daniel Reker, Petra Schneider, Gisbert Schneider, JB Brown.
+ DOI-URL: https://doi.org/10.4155/fmc-2016-0197
+
+
+ Title: Small Random Forest Models for Effective Chemogenomic Active Learning
+ Journal: Journal of Computer Aided Chemistry
+ Contributors: Christin Rakers, Daniel Reker, J.B. Brown.
+ DOI-URL: https://doi.org/10.2751/jcac.18.124
+
+
+ Title: Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing
+ Journal: PLOS Computational Biology
+ Contributors: Hansaim Lim, Aleksandar Poleksic, Yuan Yao, Hanghang Tong, Di He, Luke Zhuang, Patrick Meng, Lei Xie, .
+ DOI-URL: https://doi.org/10.1371/journal.pcbi.1005135
+
+Article title: Matched Molecular Series: Measuring SAR Similarity
+Publication date: May 1, 2017
+DOI-URL: https://doi.org/10.1021/acs.jcim.6b00709
+
+Subjects:
+Substituents, Mathematical methods, Structure activity relationship, Biological databases
+
+Contributors:
+Emanuel S. R. Ehmki, Christian Kramer
+
+This publication is cited by the following 5 publications:
+
+
+ Title: Matched Molecular Series Analysis for ADME Property Prediction
+ Journal: Journal of Chemical Information and Modeling
+ Contributors: Mahendra Awale, Sereina Riniker, Christian Kramer.
+ DOI-URL: https://doi.org/10.1021/acs.jcim.0c00269
+
+
+ Title: Approaches using AI in medicinal chemistry
+ Journal:
+ Contributors: Christian Tyrchan, Eva Nittinger, Dea Gogishvili, Atanas Patronov, Thierry Kogej.
+ DOI-URL: https://doi.org/10.1016/B978-0-12-822249-2.00002-5
+
+
+ Title: Bioactivity Prediction Based on Matched Molecular Pair and Matched Molecular Series Methods
+ Journal: Current Pharmaceutical Design
+ Contributors: Xiaoyu Ding, Chen Cui, Dingyan Wang, Jihui Zhao, Mingyue Zheng, Xiaomin Luo, Hualiang Jiang, Kaixian Chen.
+ DOI-URL: https://doi.org/10.2174/1381612826666200427111309
+
+
+ Title: BRADSHAW: a system for automated molecular design
+ Journal: Journal of Computer-Aided Molecular Design
+ Contributors: Darren V. S. Green, Stephen Pickett, Chris Luscombe, Stefan Senger, David Marcus, Jamel Meslamani, David Brett, Adam Powell, Jonathan Masson.
+ DOI-URL: https://doi.org/10.1007/s10822-019-00234-8
+
+
+ Title: The use of matched molecular series networks for cross target structure activity relationship translation and potency prediction
+ Journal: MedChemComm
+ Contributors: Christopher E. Keefer, George Chang.
+ DOI-URL: https://doi.org/10.1039/C7MD00465F
+
--
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