http://www.ncbi.nlm.nih.gov/locuslink/help.html
Locuslink Help Pubmed Entrez BLAST OMIM Taxonomy Structure Search Locuslink Maps Nucleotide OMIM Protein Pubmed Unigene Unists Display Brief Summary Organism: All Fruit_fly HIV Human Mouse Rat Zebrafish Query: Locuslink Home Collaborators Download FAQ Help Statistics NCBI Genome Guides Fruit_fly Human Mouse Rat Yeast Zebrafish Refseq About Download FAQ Statistics Related Resources BDGP CGAP Flybase GDB Genemap'99 Homologene Map Viewer--fruit_fly--human--mouse--rat--zebrafish MGD Nomenclature OMIM RATMAP RGD SGD Unigene ZFIN A_b_c D_e_f G_h_i J_k_l_m N O P_q_r S_t_u V_w_x Y Z Locuslink Help Information is available on: Query Tips Browse lists alphabetical lists or brief display format summary display format selecting records and saving as text Locus Report pages table_of_contents and selecting records saving as text Constructing URLS to Locuslink Query Tips: A multi-resource query form is_provided at the top of Locuslink pages. The Search box can be_used to query Locuslink, OMIM, Pubmed, Entrez Nucleotide, Entrez protein, human Mapview, Unigene, and Unists using symbols, names, accession numbers, or other resource-specific identifiers. Display options allow a brief report (the default), or a summary of each record that may include alternative symbols, MIM numbers, and sequence accessions. Organism options allow restricting a query to one organism (fruit_fly, human, mouse, rat, or zebrafish), or querying them all_the default). Controlled terms are_used to index certain records for special retrieval. These include: has_homol a locus associated with a Homologene record has_omim a locus associated with an OMIM record has_seq a locus associated with nucleotide sequence has_snp a locus associated with a dbsnp record disease_known a human locus associated with disease phenotype defined by a MIM number (may_be only that phenotype) seq_map either the gene or an STS in_this record has_been_localized to the sequence-based map available from Map Viewer type_dseg The locus is DNA segment. May include BAC or YAC ends. type_gene_protein the locus is a gene than encodes a protein product. Does not include unreviewed, putative genes based only on modeling; named genes that encode only part_of a protein product such_as immunoglobulin variable, diversity, joining, or constant regions; or genes that exhibit somatic rearrangement type_gene_other the locus is a gene that does not fall_into the category type_gene_protein. type_pheno The locus is_characterized a as a mapped phenotype only. type_pseudo The locus is a pseudogene. type_qtl The locus is_characterized a phenotype as a QTL only. type_region The locus is a region on the genome. Examples are_named gene clusters and viral integration site. The Locuslink query searches for any word (or word stem) in a Locuslink report. Proximity searches, searches on phrases, and synonyms are_supported not, so_that entering serine proteinase will retrieve records containing both serine and proteinase, but not necessarily serine proteinase and not records containing serine and protease but not proteinase. The query results are_returned as a summary alphabetized by Symbol (browse list). Any detailed Locuslink report page is_accessed then by clicking on the Locusid number at the left. Color-coded icons support rapid jumps to related records in ubmed, MIM, efseq, Genbank nucleotide, rotein, omologene, nigene, and ariation data (dbsnp) Summary of Query options wild card*Field restriction lower_case, no space allowed between the term and the brackets; the combination of wild card and field restriction supported only with symbol sym chr chromosome loc Locusid mim MIM number sym symbol pm Pubmed id ngi nucleotide gi pgi protein gi booleans if_not entered, and is_implied with multiple words no case sensitivity AND/and, OR/or, NOT/not are_supported all Note: Grouping by parentheses is_supported not and organism-specific restrictions are_managed by the Organism: pull_down menu. However, the order in which query terms are_added does make a difference. Query terms are_processed in_order from left to right, and the_next qery term on the right is_applied to the result of the previous operation. See_also: Constructing URLS to Locuslink Examples of Locuslink Queries Query Result A2m Browse list including A2m and IGHA2. Click on the Locusid value (2, 3494 respectively) to display each Locuslink Report. A2*Browse list of loci with words beginning with"A2"in any data field. macroglobulin Browse list of loci with the word"macroglobulin"in any data field. 2 chr Browse list of loci on chromosome 2. protein_kinase 3 chr Browse list of loci with records containing the word protein and the word kinase and a location on chromosome 3 12p1*Browse list of loci recorded as having the upper range somewhere in 12p13, 12p12, or 12p11. Note: This_is a"string"search and not a range search. Warning: Except for the field sym, wild cards cannot be_used in combination with field-restriction (e_g. mim, chr) 4. 1. 2. 13 Browse list of loci encoding enzymes with this EC number (ALDOA, ALDOB, and ALDOC. 103950 mim Browse list containing only A2m, because 103950 is the MIM number for A2m. 12305*Browse list of loci with numbers beginning 12305 (in_this case based_on MIM numbers and a GDB id) in any data field. Note: Stemming does not work with field-restricted searches (mim, chr) Hs. 74561 Browse list containing only A2m, because (Hs. 74561 is the Unigene cluster number for A2m) AF053356 Browse list of loci with sequences in_this Genbank record. Note: accession data continue to be_integrated; some valid accession numbers may_not yield a result. acad*pseudogene not 11 chr loci with records containing words starting with acad and having the word pseudogene but not on chromosome 11. Note the implied and associating acad and pseudogene. has_homol disease_known 13 chr loci on chromosome 13 with both homology data and linked to a disease phenotype in OMIM. Browsing the data Alphabetical lists and the brief display format One display format for Locuslink is the browsable list sorted by symbol. Lists are_precalculated either or returned as a query result. The precalculated lists are_separated by the first letter of a symbol, and include all genomes. Click on one of the letters of the alphabet on_the_top_of a page to review all official and alias symbols beginning with_that letter. The browse list summarizes the following attributes of each locus: Browsable Lists Data Element Definition Locusid NCBI assigns a unique, stable Locusid to each locus. Click on the number to retrieve the detailed Locuslink Report page. Note: As part_of NCBI's Genome Annotation Project, some Locuslink records may_be_generated which are likely to be temporary and which therefore are_represented not by a stable ID. Instead, each is_indicated by More, which is also to be_clicked to display the Report page. Org A two-letter abbreviation for the organism in which this locus is_described. The symbols (Hs for Homo_sapiens, Mm for Mus_musculus, Rn for Rattus_norvegicus, Dr for Danio rerio, and Dm for Drosophila_melanogaster match the abbreviations used by Unigene. Symbol The official or alias symbol. Aliases point to the official symbol. In some cases a symbol may_be an alias for multiple loci. Description The gene name. Position The cytogenetic (human or rat) or genetic (mouse) location. Links When links are available for Pubmed, OMIM, Refseq, Genbank, Homologene, Unigene and variation data, they are_indicated as small color-coded blocks. Note: Neither Pubmed nor Genbank links are comprehensive. Use the Related Articles or nucleotide neighbors functions to retrieve more records. Pubmed OMIM Refseq enbank nucleotide Protein Homologene Unigene Variation Summary display format In_addition_to the browse lists (brief display format), there_is an option on the query bar to display results in a summary format. This permits viewing not_only the accessions that underly the efseq, enbank nucleotide, and rotein buttons, but_also the other symbols (Aliases) and the MIM number (OMIM) when available. Also note that when the Refseqs for that locus have_been_reviewed, the label is Refseq R . Otherwise it is Refseq. Selecting records and displaying as text If a query results in more_than one record, you may select to see or save a subset of those records by checking the box to left of the Locusid and then pressing either View Loci to generate Locuslink reports for those records or Save Loci to provide a text display of the reports. The text is_formated as the LL_TMPL file available for ftp. See the README for a description of this format. Locuslink Reports The Locusid values presented on both the browse lists are_linked to a more detailed report page. A report page may include the following information: Genomic Diagram more... Button Links more... Nomenclature more... Overview more... Function more... Relationships more... Map Information more... NCBI Reference Sequences more... Genbank Sequences more... Additional Links more...Selecting the record to display and using the Table_of_contents Although multiple records can be_selected for a report, only one record is_displayed in the browser at_a_time. The table_of_contents for the record is_provided in the blue column at the left, and the menu selection box named view allows you to switch displays. Saving a set of reports as text The Save All Loci button generates a text display of the reports. The text is_formated as the LL_TMPL file available for ftp. See the README for a description of this format. Data Element Definition Genomic diagrams The exon/intron organization of the longest mature mrna from genes and models aligned to genomic sequence (NT_000000 accessions) is_diagrammed (5'-3')at the top of each report. Clicking on_that display opens a new window showing alignments of non-model RNAS to an NT_000000 accession. An option to see more details, via the Evidence Viewer, is_provided via the option"Go_to full display with alignments"."Button Links Buttons are_provided at the top of each report page to indicate when information may_be available from a subset of other resources. More links may_be_listed at_the_end_of the report page in the Additional Links section. Links to sites with more information Cancer Gene Anatomy Project Tumor Suppressor and Oncogene Directory Ensembl Flybase The Genome Database Human Gene_mutation Database Homologene Mapviewer Mouse Genome Database Online Mendelian Inheritance in Man Proteome, Inc. Pubmed Publications RATMAP UCSC Human Genome Project Working Draft Unigene dbsnp Variation Database Zebrafish Information Network Other links BL link to a BLINK report mv link to Mapview pm link to Pubmed for a specific concept sv link to Sequence Viewer Nomenclature Official Gene Symbol...The official symbol and full name of a gene assigned by the genome-specific nomenclature committee. Interim Gene Symbol...If the official symbol and name have NOT been_established, an interim symbol and name are_provided. Locusid...The unique NCBI Locusid assigned to each locus. Locusids are stable, genome-independent identifiers. Overview Refseq Summary Summary written by staff of the NCBI Refseq group describing the function, localization, and sequence properties of the gene and its products. Contributed Summary Summary supplied by non-Refseq staff. Type The category of the locus. Options include genes that encode proteins, genes that encode untranslated RNA, mapped phenotypes, anonymous DNA segments, models. Product The preferred gene product name. These names may_be_revised to reflect current usage. Alternate Symbols Alias symbols. These are_compiled from previous nomenclature, the published literature or sequence records. Alias Alternative product names. Function This section describes the function of the protein or RNA encoded by this locus. It may include Enzyme Commission numbers, disease names established by OMIM, and/or terms from ontologies such_as Gene Ontology (GO). When ontologies are_displayed, the information table may contain: the term a coded representation of the evidence for this annotation the source of the annotation a link to Pubmed Whenever possible, the evidence codes are_established those by GO. Code Explanation IMP inferred from mutant phenotype IGI inferred from genetic interaction IPI inferred from physical interaction ISS inferred from sequence or structural similarity IDA inferred from direct assay IEP inferred from expression pattern IEA inferred from electronic annotation TAS traceable author statement NAS non-traceable author statement NR not recorded E experimental evidence P predicted/computed EC number Enzyme commission number (s). Phenotype The name of the disease that may result from variants at this locus; this_is linked to the OMIM record for the disease Relationships This section is under development. At_present it may report human/mouse homologies and transcripts annotated on the genome (models) that are_known related_to genes. Mouse/Human Homology Map links to NCBI's Human-Mouse Homology Map which represents homologies that have_been_computed curated or by sequence homology. The link on the symbol goes to the Locuslink record of the homology, the Mm and Hs links go_to the indicated map where gene order is based_on mouse or human coordinates, respectively. Map Information Chromosome The chromosome (s) to which this locus has_been_mapped. Cytogenetic The cytogenetic position. Genetic The genetic position. Markers STS markers determined to be_associated with this locus. These associations are_established either (1) computationally by epcr with mrnas associated with this locus_id,(3) computationally from the NCBI's Genome Annotation based_on STS lying within the region defined by a Locusid, or (3) in a published citation. If the STS is_mapped, that location is_given also. The marker name links to dbsts reports. mv: link to STS on Map Viewer pm: link to Pubmed for paper providing details about the relationship between this locus and this marker NCBI Reference Sequences (Refseq ) All Refseq records created for a given locus are_listed. Multiple records are_distinguished by the brief description of the transcript variant. more... and Refseq FAQ This section provides links to: the Refseq nucleotide record (genomic and mrna accessions have'NG_'and'NM_'prefixes, respectively) the Refseq protein record (the'NP_'prefix) the CD browser report for each domain found in the Refseq the Genbank source sequence (s ) used to construct the Refseq record BL provides a quick link to the BLINK result for the protein. In_addition_to providing links to the sequence and for contigs and models, the genome annotation section also provides these links: sv to the graphic display mode of the NCBI sequence viewer ev to the graphic display (evidence viewer) of mrnas aligning to the NT_ accesssion in the region of the gene, with reports of mismatches, insertions, and deletions relative to_that genomic sequence for accessions not derived from the NT_ accession (namely NM_ Refseqs and Genbank accessions) Genbank Sequences A table of a subset of representative nucleotide and protein accessions for the locus. These accessions are_derived initially from a variety of collaborations. These data are_included in our review processes and the accessions listed for a given locus may change_over time. EST accession numbers are_provided if no other sequence data are available to represent the locus. Type: Molecule type for the nucleotide record. m mrna g genomic DNA e EST u undetermined Protein accessions are_linked to Entrez sequence displays . BL provides a quick link to the BLINK result for the protein. Strain data, as annotated on the Genbank record, is_displayed when available. Additional Links This section names and provides links to additional sites that may contain information related_to this locus. OMIM The MIM number assigned to this gene product. Unigene The Unigene cluster that represents this locus . Constructing URLS to Locuslink To create a link to Locuslink, use the syntax: http://www. ncbi. nlm. nih. gov/Locuslink/request Where request can be_constructed to support the following: a search a link to a specific record a link to one or more Locusid Creating a link that performs a search list. cgi? Q=term species abbreviation display option term the query as it would be_entered in the query box, including*as a wild card, for field specification species abbreviation Dm for fruit_fly Hs for human Mm for mouse Rn for rat Dr for zebrafish Notes: If ORG=is_supplied not, results for all species will_be_returned. To query more_than one but not all organisms, use ORG=for each display option 0 for brief 1 for summary Examples http://www. ncbi. nlm. nih. gov/Locuslink/list. cgi? Q=abc*looks for a record with a word beginning abc, in human (Hs) or mouse (Mm) and displayed in the brief format. Note that the organism box will show only human (the first alphabetically), even_though both were_used in the query. http://www. ncbi. nlm. nih. gov/Locuslink/list. cgi? Q=stx2 sym looks for a record with the symbol stx2, from any species, and displayed in the summary format http://www. ncbi. nlm. nih. gov/Locuslink/list. cgi? Q=abcc1 sym+OR+abcc2 sym looks for records with either the symbol abcc1 or abcc2, from any species, and displayed in the brief format Linking to a specific record Locrpt. cgi? l=Locusid Locusid the unique identifier NCBI has_assigned to this locus Example www. ncbi. nlm. nih. gov /Locuslink/Locrpt. cgi? l=12345 Returns a Locus Report for the locus with the Locusid of 12345 Linking to one or more Locusids list. cgi? ID=Locusid_1 Locusid_2 display option Locrpt. cgi? l=Locusid, Locusid, Locusid Examples list. cgi? retrieves records with these Locusid values. ORG is_ignored . If V=is_supplied not, V=0 is_used. Locrpt. cgi? l=1, 10,100, 1000 generates a report for Locusid=1, and provides a menu to allow display of Locusids 10,100, or 1000 without doing another query. Collects these report for saving as text Last modified: Wednesday March 6 2002 Questions or Comments? Write to the Help Desk Disclaimer Privacy statement NCBI NLM NIH Top of page