{"id":23057427,"url":"https://github.com/codebiogenomics/pubmed-analyzer","last_synced_at":"2025-08-15T06:32:43.036Z","repository":{"id":262142689,"uuid":"845680131","full_name":"applicativesystem/pubmed-analyzer","owner":"applicativesystem","description":"analyzing pubmed articles for natural language processing. ","archived":false,"fork":false,"pushed_at":"2024-08-21T19:01:16.000Z","size":2,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-11-10T20:18:19.651Z","etag":null,"topics":["bioinformatics","genome-analysis","language-model","language-processing","literature-management","literature-mining","pubmed","python3"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/applicativesystem.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-08-21T18:04:37.000Z","updated_at":"2024-09-11T13:27:42.000Z","dependencies_parsed_at":"2024-11-10T20:18:28.002Z","dependency_job_id":"38bde0dc-5a40-433c-a81e-318df158b7ab","html_url":"https://github.com/applicativesystem/pubmed-analyzer","commit_stats":null,"previous_names":["applicativesystem/pubmed-analyzer"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fpubmed-analyzer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fpubmed-analyzer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fpubmed-analyzer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fpubmed-analyzer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/applicativesystem","download_url":"https://codeload.github.com/applicativesystem/pubmed-analyzer/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":229897445,"owners_count":18141135,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","genome-analysis","language-model","language-processing","literature-management","literature-mining","pubmed","python3"],"created_at":"2024-12-16T02:12:17.035Z","updated_at":"2025-08-15T06:32:38.950Z","avatar_url":"https://github.com/applicativesystem.png","language":"Python","readme":"# pubmed-abstract-fetcher\n\n- This function will prepare the abstract and the id information for all the [pubmed](https://pubmed.ncbi.nlm.nih.gov) articles that you want to read and have as a citation.\n- I coded this using a web scraping approach and it is blazing fast and parses better than ncbi eutils.\n- You can give any ncbi pubmed id single or pass it through the file and it will download and prepare the citations, abstract and also the corpus for the language data.\n\n```python\nncbiAbstractMiner()\n[('18980659',\n  'The Arabidopsis thaliana genome contains hundreds of genes essential for seed development.\nBecause null mutations in these genes cause embryo lethality,  their specific molecular and developmental\nfunctions are largely unknown. Here, we identify a role for EMB1611/MEE22, an essential\ngene in Arabidopsis, in shoot apical meristem maintenance. EMB1611 encodes a large,\nnovel protein with N-terminal coiled-coil regions and two putative transmembrane domains.\nWe show that the partial loss-of-function emb1611-2 mutation causes a range of pleiotropic\ndevelopmental phenotypes, most dramatically a progressive loss of shoot apical meristem\nfunction that causes premature meristem termination. emb1611-2 plants display disorganization\nof the shoot meristem cell layers early in development, and an associated stem cell\nfate change to an organogenic identity. Genetic and molecular analysis indicates\nthat EMB1611 is required for maintenance of the CLV-WUS stem cell regulatory pathway\nin the shoot meristem, but also has WUS-independent activity. In addition,\nemb1611-2 plants have reduced shoot and root growth, and their rosette leaves form trichomes with extra branches,\n a defect we associate with an increase in endoreduplication. Our data indicate\nthat EMB1611 functions to maintain cells, particularly those in the shoot meristem,\nroots and developing rosette leaves, in a proliferative or uncommitted state.')]\n```\n\n```python\nncbiAbstractMiner(file)\nYou can pass a file with endless pubmed ids.\n```\n\nGaurav Sablok \\\nUniversity of Potsdam \\\nPotsdam,Germany\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcodebiogenomics%2Fpubmed-analyzer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcodebiogenomics%2Fpubmed-analyzer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcodebiogenomics%2Fpubmed-analyzer/lists"}