cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25549/webster-c100-15018
title: Area Resources Management Guide, 1980-1992

description: A reference book developed in order to provide area commanders and supervisory managers with a training tool and a guide to assist them in managing departmental resources, 1980-1992. PART OF SERIES: In its probe of LAPD operations, the Webster Commission surveyed the emergency procedures of other major cities in the United States, many of which had experienced similar instances of civil unrest. The series contains materials that were acquired and studied by the Commission for this purpose. Included are reference guides developed by several police departments that delineate their structure, rules, and policies; manuals that outline emergency operations plans and procedures; reports that discuss the role of community-oriented policing in the prevention of crime; and assessments of the police departments response to riots in other cities. PART OF SUBSERIES: Materials related to police plans, procedures, and operations of the California Highway Patrol.
DOI: 10.25549/webster-c100-17096
title: Resolution ratifying the existence of a local emergency, 1992

description: Resolution Ratifying the Existence of a Local Emergency due to Civil Disturbance in the City of Los Angeles and the Need for Continuing State of Local Emergency, by the city of Los Angeles. A resolution adopted by the Los Angeles City Council, in light of the 1992 riots, which ratified the existence of a local emergency and the need for continuing the state of local emergency, 1992. PART OF SERIES: In its investigation, the Webster Commission aligned the policies and procedures of the LAPD with those adopted by several other agencies and governmental bodies. The series contains a variety of materials collected by the Commission for this purpose. Included are reports about present and future issues facing the City of Los Angeles; analyses of riots which shook Washington, D.C. in 1968; annual reports issued by the Royal Canadian Mounted Police; emergency plans; housing data; newspaper and journal articles; criminal justice statistics; and summaries and after-action reports which assessed law enforcement's response to the 1992 riots.
DOI: 10.25549/webster-c100-17105
title: Resolution ratifying the existence of a local emergency, 1992

description: Resolution Ratifying the Existence of a Local Emergency due to Civil Disturbance in the City of Los Angeles and the Need for Continuing State of Local Emergency, by the city of Los Angeles. A resolution adopted by the Los Angeles City Council, in light of the 1992 riots, which ratified the existence of a local emergency and the need for continuing the state of local emergency, 1992. PART OF SERIES: In its investigation, the Webster Commission aligned the policies and procedures of the LAPD with those adopted by several other agencies and governmental bodies. The series contains a variety of materials collected by the Commission for this purpose. Included are reports about present and future issues facing the City of Los Angeles; analyses of riots which shook Washington, D.C. in 1968; annual reports issued by the Royal Canadian Mounted Police; emergency plans; housing data; newspaper and journal articles; criminal justice statistics; and summaries and after-action reports which assessed law enforcement's response to the 1992 riots.
DOI: 10.25549/webster-c100-16593
title: Emergency procedures, Atlanta, 1985

description: Chain of command and standard operating procedures during unusual occurrences and states of emergency, 1985. PART OF SERIES: In its probe of LAPD operations, the Webster Commission surveyed the emergency procedures of other major cities in the United States, many of which had experienced similar instances of civil unrest. The series contains materials that were acquired and studied by the Commission for this purpose. Included are reference guides developed by several police departments that delineate their structure, rules, and policies; manuals that outline emergency operations plans and procedures; reports that discuss the role of community-oriented policing in the prevention of crime; and assessments of the police departments response to riots in other cities. PART OF SUBSERIES: Materials related to police plans, procedures, and operations in Atlanta, Georgia.
DOI: 10.25549/webster-c100-77791
title: LAPD Personnel Interviews, Albanese - Hutjens, 1992

description: Analysis of the Los Angeles Police Department's planning, preparedness and response to the 1992 riot ( the first six hours), Los Angeles Police Department personnel interviews, Michael A. Albanese - Lisa M. Hutjens, 1992. PART OF SERIES: Included in the series are internal documents produced by the LAPD, which aided the Webster Commission in its assessment of the Department's operations. Materials include copies of the Watch Commander's Daily Reports between October, 1991 and May, 1992; critiques and after-action reports on the riots issued by each LAPD bureau; and correspondence regarding personnel and budget matters, crime statistics, and several Department-initiated programs. Also included are several documents, including schedules, press releases, and memoranda, that were issued by the office of Los Angeles Mayor Tom Bradley regarding the verdicts in the Rodney King case.
DOI: 10.25549/webster-c100-27684
title: Police, 1973-01-23

description: A report by the National Advisory Commission on Criminal Justice Standards and Goal's Task Force on Police that offers national guidelines for police and law enforcement personnel, 1973 January 23. PART OF SERIES: Materials in the series assess a number of policies, plans, and procedures in place prior to the 1992 Los Angeles riots, many of which arguably contributed to the social upheaval. Included are several reports produced by the International Association of Chiefs of Police about model law enforcement policy; reports that address deficiencies in police-community relations in Los Angeles; emergency operations and recovery plans developed by the City of Los Angeles; demographic analyses of the city's public housing developments; and a Los Angeles Times publication assessing the riots' root causes. Also included are statistics released by the Los Angeles Department of Building and Safety about structural damage incurred as a result of the violence and looting.
DOI: 10.25549/webster-ouc11441620
title: LAPD Harbor area personnel roster and standing plans, 1992-05-14

description: Los Angeles Police Department Harbor area personnel roster and standing plans, 1992 May 14. PART OF SERIES: This series consists of materials related to the LAPD's emergency and disaster planning measures. Included are standing plans, mobilization records, and rally points from several of the LAPD's geographic divisions, as well as manuals, lesson plans, and curricula developed by the LAPD for emergency procedures.
DOI: 10.25549/webster-c100-27543
title: Police, 1973-01-23

description: A report by the National Advisory Commission on Criminal Justice Standards and Goal's Task Force on Police that offers national guidelines for police and law enforcement personnel, 1973 January 23. PART OF SERIES: Materials in the series assess a number of policies, plans, and procedures in place prior to the 1992 Los Angeles riots, many of which arguably contributed to the social upheaval. Included are several reports produced by the International Association of Chiefs of Police about model law enforcement policy; reports that address deficiencies in police-community relations in Los Angeles; emergency operations and recovery plans developed by the City of Los Angeles; demographic analyses of the city's public housing developments; and a Los Angeles Times publication assessing the riots' root causes. Also included are statistics released by the Los Angeles Department of Building and Safety about structural damage incurred as a result of the violence and looting.
DOI: 10.5281/zenodo.14042229
title: Scorpio Gene-Taxa Benchmark Dataset2 (Short Fragments)

description: We used the Woltka pipeline to compile the complete Basic genome dataset, consisting of 4634 genomes, with each genus represented by a single genome. After downloading all coding sequences (CDS) from the NCBI database, we extracted 8 million distinct CDS, focusing on bacteria and archaea and excluding viruses and fungi due to inadequate gene information.

To maintain accuracy, we excluded hypothetical proteins, uncharacterized proteins, and sequences without gene labels. We addressed issues with gene name inconsistencies in NCBI by keeping only genes with more than 1000 samples and ensuring each phylum had at least 350 sequences. This resulted in a curated dataset of 800,318 gene sequences from 497 genes across 2046 genera.

We created four datasets to evaluate our model: a training set (Train_set), a test set (Test_set) with different samples but the same genus and gene as the training set, a Taxa_out_set excluding 18 phyla present in the training set but from different phyla, and a Gene_out_set excluding 60 genes from the training set but from the same phyla. We ensured each CDS had only one representation per genome, removing genes with multiple representations within the same species.

 

We derived 400bp fragments from the 800k-sequence gene dataset. Our method involved selecting randomly  400bp segments from different regions within each gene sequence, ensuring at least a 50bp gap between consecutive fragments. This was achieved within the range Range: [0, Gap: 50, length(gene_sequence)]. We chose this approach to avoid fragments with minimal base-pair differences and to replicate sequences that may not necessarily begin with an open reading frame.


 

Technical info





test.fasta :  Contains sequences for model testing.




gene_out.fasta: Includes sequences excluded based on gene criteria for model evaluation.




taxa_out.fasta :Includes sequences excluded based on taxonomic criteria for model evaluation.


val.fasta: Contains sequences for model validation .



train.fasta: Contains sequences for model training.




meta_data.csv: Contains metadata information for sequences in the FASTA files.




hierarchical-level.txt : Determines hierarchical levels for triplet training and hierarchical sampling required for Scorpio training.



 

 

@article{refahi2024scorpio,
  title={Scorpio: Enhancing Embeddings to Improve Downstream Analysis of DNA sequences},
  author={Refahi, Mohammadsaleh and Sokhansanj, Bahrad A and Mell, Joshua Chang and Brown, James and Yoo, Hyunwoo and Hearne, Gavin and Rosen, Gail},
  journal={bioRxiv},
  pages={2024--07},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}
DOI: 10.5281/zenodo.14042230
title: Scorpio Gene-Taxa Benchmark Dataset2 (Short Fragments)

description: We used the Woltka pipeline to compile the complete Basic genome dataset, consisting of 4634 genomes, with each genus represented by a single genome. After downloading all coding sequences (CDS) from the NCBI database, we extracted 8 million distinct CDS, focusing on bacteria and archaea and excluding viruses and fungi due to inadequate gene information.

To maintain accuracy, we excluded hypothetical proteins, uncharacterized proteins, and sequences without gene labels. We addressed issues with gene name inconsistencies in NCBI by keeping only genes with more than 1000 samples and ensuring each phylum had at least 350 sequences. This resulted in a curated dataset of 800,318 gene sequences from 497 genes across 2046 genera.

We created four datasets to evaluate our model: a training set (Train_set), a test set (Test_set) with different samples but the same genus and gene as the training set, a Taxa_out_set excluding 18 phyla present in the training set but from different phyla, and a Gene_out_set excluding 60 genes from the training set but from the same phyla. We ensured each CDS had only one representation per genome, removing genes with multiple representations within the same species.

 

We derived 400bp fragments from the 800k-sequence gene dataset. Our method involved selecting randomly  400bp segments from different regions within each gene sequence, ensuring at least a 50bp gap between consecutive fragments. This was achieved within the range Range: [0, Gap: 50, length(gene_sequence)]. We chose this approach to avoid fragments with minimal base-pair differences and to replicate sequences that may not necessarily begin with an open reading frame.


 

Technical info





test.fasta :  Contains sequences for model testing.




gene_out.fasta: Includes sequences excluded based on gene criteria for model evaluation.




taxa_out.fasta :Includes sequences excluded based on taxonomic criteria for model evaluation.


val.fasta: Contains sequences for model validation .



train.fasta: Contains sequences for model training.




meta_data.csv: Contains metadata information for sequences in the FASTA files.




hierarchical-level.txt : Determines hierarchical levels for triplet training and hierarchical sampling required for Scorpio training.



 

 

@article{refahi2024scorpio,
  title={Scorpio: Enhancing Embeddings to Improve Downstream Analysis of DNA sequences},
  author={Refahi, Mohammadsaleh and Sokhansanj, Bahrad A and Mell, Joshua Chang and Brown, James and Yoo, Hyunwoo and Hearne, Gavin and Rosen, Gail},
  journal={bioRxiv},
  pages={2024--07},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}
DOI: 10.25549/webster-ouc11441635
title: LAPD Harbor area personnel roster and standing plans, 1992-05-14

description: Los Angeles Police Department Harbor area personnel roster and standing plans, 1992 May 14. PART OF SERIES: This series consists of materials related to the LAPD's emergency and disaster planning measures. Included are standing plans, mobilization records, and rally points from several of the LAPD's geographic divisions, as well as manuals, lesson plans, and curricula developed by the LAPD for emergency procedures.
DOI: 10.25549/webster-c100-27635
title: Police, 1973-01-23

description: A report by the National Advisory Commission on Criminal Justice Standards and Goal's Task Force on Police that offers national guidelines for police and law enforcement personnel, 1973 January 23. PART OF SERIES: Materials in the series assess a number of policies, plans, and procedures in place prior to the 1992 Los Angeles riots, many of which arguably contributed to the social upheaval. Included are several reports produced by the International Association of Chiefs of Police about model law enforcement policy; reports that address deficiencies in police-community relations in Los Angeles; emergency operations and recovery plans developed by the City of Los Angeles; demographic analyses of the city's public housing developments; and a Los Angeles Times publication assessing the riots' root causes. Also included are statistics released by the Los Angeles Department of Building and Safety about structural damage incurred as a result of the violence and looting.
DOI: 10.25549/webster-c100-14709
title: Departmental Training, 1980-06

description: A training manual developed by the California Highway Patrol, 1980 June. PART OF SERIES: In its probe of LAPD operations, the Webster Commission surveyed the emergency procedures of other major cities in the United States, many of which had experienced similar instances of civil unrest. The series contains materials that were acquired and studied by the Commission for this purpose. Included are reference guides developed by several police departments that delineate their structure, rules, and policies; manuals that outline emergency operations plans and procedures; reports that discuss the role of community-oriented policing in the prevention of crime; and assessments of the police departments response to riots in other cities. PART OF SUBSERIES: Materials related to police plans, procedures, and operations of the California Highway Patrol.
DOI: 10.25549/webster-c100-16770
title: Emergency Incident Guide, 1992-04

description: A reference book for uniformed personnel who are first responders to an emergency scene and managers of emergency incidents and disasters, 1992 April. PART OF SERIES: In its probe of LAPD operations, the Webster Commission surveyed the emergency procedures of other major cities in the United States, many of which had experienced similar instances of civil unrest. The series contains materials that were acquired and studied by the Commission for this purpose. Included are reference guides developed by several police departments that delineate their structure, rules, and policies; manuals that outline emergency operations plans and procedures; reports that discuss the role of community-oriented policing in the prevention of crime; and assessments of the police departments response to riots in other cities. PART OF SUBSERIES: Materials related to police plans, procedures, and operations of the California Highway Patrol.
DOI: 10.25549/webster-c100-16755
title: Emergency Incident Guide, 1992-04

description: A reference book for uniformed personnel who are first responders to an emergency scene and managers of emergency incidents and disasters, 1992 April. PART OF SERIES: In its probe of LAPD operations, the Webster Commission surveyed the emergency procedures of other major cities in the United States, many of which had experienced similar instances of civil unrest. The series contains materials that were acquired and studied by the Commission for this purpose. Included are reference guides developed by several police departments that delineate their structure, rules, and policies; manuals that outline emergency operations plans and procedures; reports that discuss the role of community-oriented policing in the prevention of crime; and assessments of the police departments response to riots in other cities. PART OF SUBSERIES: Materials related to police plans, procedures, and operations of the California Highway Patrol.
DOI: 10.25549/webster-c100-14710
title: Departmental Training, 1980-06

description: A training manual developed by the California Highway Patrol, 1980 June. PART OF SERIES: In its probe of LAPD operations, the Webster Commission surveyed the emergency procedures of other major cities in the United States, many of which had experienced similar instances of civil unrest. The series contains materials that were acquired and studied by the Commission for this purpose. Included are reference guides developed by several police departments that delineate their structure, rules, and policies; manuals that outline emergency operations plans and procedures; reports that discuss the role of community-oriented policing in the prevention of crime; and assessments of the police departments response to riots in other cities. PART OF SUBSERIES: Materials related to police plans, procedures, and operations of the California Highway Patrol.
DOI: 10.25549/webster-c100-77858
title: LAPD Personnel Interviews, Albanese - Hutjens, 1992

description: Analysis of the Los Angeles Police Department's planning, preparedness and response to the 1992 riot ( the first six hours), Los Angeles Police Department personnel interviews, Michael A. Albanese - Lisa M. Hutjens, 1992. PART OF SERIES: Included in the series are internal documents produced by the LAPD, which aided the Webster Commission in its assessment of the Department's operations. Materials include copies of the Watch Commander's Daily Reports between October, 1991 and May, 1992; critiques and after-action reports on the riots issued by each LAPD bureau; and correspondence regarding personnel and budget matters, crime statistics, and several Department-initiated programs. Also included are several documents, including schedules, press releases, and memoranda, that were issued by the office of Los Angeles Mayor Tom Bradley regarding the verdicts in the Rodney King case.
DOI: 10.25549/webster-c100-33830
title: Correspondence, interviews, 1992-05/1992-09

description: Correspondence and memoranda from several sources about conducting interviews in regards to the 1992 riots; surveys about the practices and policies of police departments in regards to planning for and responding to outbreaks of civil disturbance, 1992 May-September. PART OF SERIES: After the violence had subsided, the Webster Commission met of a variety of public officials, law enforcement personnel, activists, and community leaders to discuss the rioting, its root causes, and the adequacy of the LAPD's response. The series includes summaries of these meetings, including questions and comments along of the interviewers' own mental impressions, conclusions, and opinions. Materials are arranged in alphabetical order, according to the last name of the interviewee.
DOI: 10.25549/webster-c100-77924
title: LAPD Personnel Interviews, Albanese - Hutjens, 1992

description: Analysis of the Los Angeles Police Department's planning, preparedness and response to the 1992 riot ( the first six hours), Los Angeles Police Department personnel interviews, Michael A. Albanese - Lisa M. Hutjens, 1992. PART OF SERIES: Included in the series are internal documents produced by the LAPD, which aided the Webster Commission in its assessment of the Department's operations. Materials include copies of the Watch Commander's Daily Reports between October, 1991 and May, 1992; critiques and after-action reports on the riots issued by each LAPD bureau; and correspondence regarding personnel and budget matters, crime statistics, and several Department-initiated programs. Also included are several documents, including schedules, press releases, and memoranda, that were issued by the office of Los Angeles Mayor Tom Bradley regarding the verdicts in the Rodney King case.
DOI: 10.25549/webster-c100-33571
title: Correspondence, interviews, 1992-05/1992-09

description: Correspondence and memoranda from several sources about conducting interviews in regards to the 1992 riots; surveys about the practices and policies of police departments in regards to planning for and responding to outbreaks of civil disturbance, 1992 May-September. PART OF SERIES: After the violence had subsided, the Webster Commission met of a variety of public officials, law enforcement personnel, activists, and community leaders to discuss the rioting, its root causes, and the adequacy of the LAPD's response. The series includes summaries of these meetings, including questions and comments along of the interviewers' own mental impressions, conclusions, and opinions. Materials are arranged in alphabetical order, according to the last name of the interviewee.
DOI: 10.25549/webster-c100-15016
title: Area Resources Management Guide, 1980-1992

description: A reference book developed in order to provide area commanders and supervisory managers with a training tool and a guide to assist them in managing departmental resources, 1980-1992. PART OF SERIES: In its probe of LAPD operations, the Webster Commission surveyed the emergency procedures of other major cities in the United States, many of which had experienced similar instances of civil unrest. The series contains materials that were acquired and studied by the Commission for this purpose. Included are reference guides developed by several police departments that delineate their structure, rules, and policies; manuals that outline emergency operations plans and procedures; reports that discuss the role of community-oriented policing in the prevention of crime; and assessments of the police departments response to riots in other cities. PART OF SUBSERIES: Materials related to police plans, procedures, and operations of the California Highway Patrol.