This is a collection of code written by Maurice Curran that was used to process the Microscopy and Microanalysis conference proceeding corpus into word products described in the publication "NLP-Driven Electron Microscopy Ontology Development". The scripts are written in Python, to be used in the following order:1. SettingUpTextFiles.py and CopyingText.py to get the raw text files; 2. SentenceConversion.py; 3. reference_remover.py; 4. testing.py and testingavg.py; 5. SentenceCreator.py; 6. matscholar_model.py to get matscholar tags; 7. training_model_gensim.py to get gensim model;8. word2vecscript.py and gensim_visual.py;

Ontology for use in Phenotyping Natural Language Processing (NLP)

Ontology for use in Phenotyping Natural Language Processing (NLP)

Ontology for use in Phenotyping Natural Language Processing (NLP)

Ontology for use in Phenotyping Natural Language Processing (NLP)

Ontology for use in Phenotyping Natural Language Processing (NLP)

The SKR Project was initiated at NLM in order to develop programs to provide usable semantic representation of biomedical free text by building on resources currently available at the library. The SKR project is concerned with reliable and effective management of the information encoded in natural language texts. The project develops programs that provide usable semantic representation of biomedical text by building on resources currently available at the Library, especially the UMLS knowledge sources and the natural language processing tools provided by the SPECIALIST system. This Java-based API to the Semantic Knowledge Representation (SKR) Scheduler facility was created to provide users with the ability to programmatically submit jobs to the Scheduler Batch and Interactive facilities instead of using the Web-based interface.

MetaMap is a highly configurable application developed by the Lister Hill National Center for Biomedical Communications at the National Library of Medicine (NLM) to map biomedical text to the UMLS Metathesaurus or, equivalently, to identify Metathesaurus concepts referred to in English text. MetaMap employs a knowledge-intensive approach, natural-language processing (NLP), and computational-linguistic techniques, and is used worldwide in industry and academia. At NLM, MetaMap is one of the foundations of NLM's Medical Text Indexer (MTI), which is applied to both semiautomatic and fully automatic indexing of biomedical literature. Technical documentation at http://metamap.nlm.nih.gov/#Downloads

This code repository contains the "back-end" of the Nexus Microscopy Facility Laboratory Information Management System (NexusLIMS), developed by the NIST Office of Data and Informatics. Its primary function is to build XML-formatted research experiment records by combining metadata from many different sources (reservation systems, the collected data files, a session logger, etc.). These records are structured according to the "Nexus Experiment" schema, meaning they can be loaded into a repository and used for structured data queries.

This code repository contains the "back-end" of the Nexus Microscopy Facility Laboratory Information Management System (NexusLIMS), developed by the NIST Office of Data and Informatics. Its primary function is to build XML-formatted research experiment records by combining metadata from many different sources (reservation systems, the collected data files, a session logger, etc.). These records are structured according to the "Nexus Experiment" schema, meaning they can be loaded into a repository and used for structured data queries.