Editing guidelines
From WikiProtein
[edit] Types of concept entries
Mrs. Hala Elraei
there are entries for authors and publications (coming soon).
[edit] The meaning of "viewpoints"
[edit] Authorizing the data for people entries
Each author has the possibility to authorize an entry. That is, an author can claim to be the authority on those specific data (publications, concepts of interest, aliases) that represent her/him. All edits by the author authority will be saved in a special viewpoint, User.
To authorize an entry, click on the link at the top of the page. You will need identify yourself to the system by logging in or, for first time editors, creating an account. Then you can go back to your data and personalize it. You can add or remove aliases, concepts of interest, publications, reference information, and tags.
[edit] Adding free text comments to a concept entry
Free text can be added to many different sections of the entry but free text cannot be added to ALL sections.
If you want to add textual comments about functional information, first you must open the edit tab for your concept of interest and find the functional information section. Clicking open the section should show two subsections: Link to other concepts and Add free text. Open the 'Add free text' subsection and you will see a table with columns labeled 'Remove', 'Connection', 'Text', 'Reference information', and several columns with the titles of the different contributors (Community, Swiss-Prot, NLM, etc).
To add a free text comment, you must choose a 'Connection' that is appropriate for your comment. The 'Connection' is found in the roll-down menu following the 'Remove' column and before the 'Text' column. The 'Connection' indicates how the free text comment relates to the concept entry. In the functional information section, often you find that the connection 'has function' accompanies many textual comments, or if it is the concept entry for an enzyme, the connection 'enzyme regulation by' may precede the textual comment. A 'Connection' must be chosen to accompany the comment or else it will not be saved. After the text is added in the text box, scroll down to the bottom and click 'Save'.
To remove a comment checking the box in the 'Remove' column and then clicking 'Save' at the bottom of the page will remove the row of data from the community view.
[edit] Adding connections between concept entries
Connections can be made to other concept entries in WikiProfessional.
New connections can be added in edit mode in any subsection that says 'Link to other concepts' or in any place that offers a roll-down menu. First, let's look at the 'Link to other concepts'. Clicking the plus/expand sign for the 'Link to other concepts' subsection, opens a table with the columns 'Remove', 'Connection', 'Other concept', 'Reference information', and several columns with the titles of the different contributors (Community, Swiss-Prot, NLM, etc).
To add a connection to another concept entry, you must choose from the first roll-down menu (in the column 'Connection') a suitable connection between the wiki concept you are editing and another wiki entry. In the second roll-down menu, the column labeled 'Other concept', you choose a second wiki concept.
To remove a connection to another concept, checking the box in the 'Remove' column and then clicking 'Save' at the bottom of the entry will remove the row of data from the community view.
[edit] Adding reference information
For every edit, it is possible to add a reference.
For example, if you see data present in an entry that is supported by one of your own publications, start by clicking the edit tab. Find the data that you would like to reference with your own publication and click the blue "Reference Information" link. Open "Link to other Web sites" and select PubMed from the drop down. In the box labeled URL, paste the url for your abstract (find your abstract on PubMed and copy the URL). A label can be added as a short description. Then click "Save" at the bottom. Voila! You've added a reference.
[edit] Adding new concepts
Adding a new concept to WikiProfessional is easy, but first search thoroughly to determine that you are not adding a concept that is already present. It is important to look for all possible synonyms of your concept before adding something new because it is not helpful to create redundant concepts. To conduct a thorough search with a variety of synonyms use the button "Search" instead of "Go".
Certain concepts share the same preferred term but have entirely different meanings (homonyms), for example, jaguar (animal) and jaguar (automobile). These concepts should be separate entries. The definition and tags should always be entered when a homonym is added to WikiProfessional to allow the concepts to be distinguished from each other.
To add a new concept, enter it in the search box and click "search". A search page will be returned that has an advanced search box at the top, a function in the middle for adding new concepts, and the words matching your search below. If you see your concept in the result list, it is already present in WikiProfessional, select it, and you can begin editing right away. If it is not in the list, then click the "create" button that is either above or below the result list.
[edit] Details on specific sections of people entries
[edit] Entry title
Searching in system, you may find that there are two entries that describe you. One entry with a title that shows your full first name, maybe your middle initial, and your last name. This is compared to one entry with a title that only shows your initials and last name. The entries with titles containing a full first name represent disambiguated authors. That is, all publications on those entries pertain specifically to those authors. Non-disambiguated entries are those that show authors represented only by their initials. For these non-disambiguated entries, it was not possible with 100% certainty to assign the publications correctly, therefore these entries may contain a mixture of publications by different authors with similar names.
[edit] Short Bio
Free text can be added to the short bio field.
Open the edit tab and then the section titled 'Short bio'. In the box labeled 'Text' add the relevant biographical details. Then scroll down to the bottom of the page and click the 'Save' button. Before clicking 'Save', it is also possible, but not necessary, to write a short note in the 'Summary' box (next to the 'Save' button) to briefly indicate the changes you've made to the entry.
[edit] Also known as
In the 'Also known as' section, it is possible to enter alternate forms of your name. There are usually a few different forms of a persons name. These forms may include the full first name, the middle initial and last name or first and middle initial and last name or last name, full first name or last name, first initial. Entering the various forms of your name can help the disambiguation of closely related names so that your work can be appropriately attributed to you.
Also in the 'also known as' section, there are 3 other possible features that can be attached to each name. These are: synonym scope, preferred in, and reference information. These features normally are applied to scientific concepts but if desired they can also be added to variations of names. Synonym scope is used to indicate whether a specific synonym is a broad synonym, narrow synonym, exact synonym or related synonym. The 'preferred in' feature indicates the specific context where the synonym is used. For scientific concepts, 'preferred in' will usually specify that the synonym is the preferred term for a specific domain. For people, 'preferred in' can be used to indicate if the name is used in a professional or familiar context. The 'reference information' is usually used to give evidence for the entered synonym.
The specific synonym must be saved before data for 'synonym scope', 'preferred in' and 'reference information' can be added to these features. To save, scroll down to the bottom of the page and click the 'Save' button. Before clicking 'Save', it is also possible, but not necessary, to write a short note in the 'Summary' box (above the 'Save' button) to briefly indicate the changes you've made to the page.
1: Singhal S, Jain S, Singla M, Pippal RB, Gondal R, Agarwal A, Kar P. Multifocal epitheloid hemangioendothelioma of liver after long-term oral contraceptive use-a case report and discussion of management difficulties encountered. J Gastrointest Cancer. 2009;40(1-2):59-63. Epub 2009 Aug 27. PubMed PMID: 19711203.
2: Singhal S, Chakravarty A, Das BC, Kar P. Tumour necrosis factor-alpha and soluble Fas ligand as biomarkers in non-acetaminophen-induced acute liver failure. Biomarkers. 2009 Aug;14(5):347-53. PubMed PMID: 19505222.
3: Singhal S, Gray T, Grace G, Verma A, Anand K. Sevoflurane Hepatotoxicity: A Case Report of Sevoflurane Hepatic Necrosis and Review of the Literature. Am J Ther. 2009 May 19. [Epub ahead of print] PubMed PMID: 19455019.
4: Singhal S, Kohaar I, Bharadwaj M, Shukla DK, Das BC, Kar P. Association of Tumor Necrosis Factor-Alpha Gene Promoter Polymorphisms with Acute Viral Hepatitis in the Indian Population. Dig Dis Sci. 2009 Apr 24. [Epub ahead of print] PubMed PMID: 19390969.
5: Singhal S, Jain S, Kohaar I, Singla M, Gondal R, Kar P. Apoptotic mechanisms in fulminant hepatic failure: potential therapeutic target. Appl Immunohistochem Mol Morphol. 2009 Jul;17(4):282-5. PubMed PMID: 19077906.
6: Singhal S, Kar P. Management of acid- and alkali-induced esophageal strictures in 79 adults by endoscopic dilation: 8-years' experience in New Delhi. Dysphagia. 2007 Apr;22(2):130-4. Epub 2007 Feb 14. PubMed PMID: 17347906.
7: Singhal S, Kar P. Corrosive injuries of esophagus and stomach--issues in management. Trop Gastroenterol. 2006 Jan-Mar;27(1):34-40. Review. PubMed PMID: 16910059.
[edit] Co-author
The co-author section links to entries of your co-authors. The co-author list is derived from your publications and cannot be modified. If some of your publications are added or removed, the co-author list will change accordingly. The co-authors shown with the full first and last name are those that have been disambiguated and have a set of correctly assigned publications. The co-authors that are shown with only first and middle initials are entries that need to be reviewed.
[edit] Reference information
In the Reference information section you can add links to other websites. For instance, if you have a personal or department home page and you would like to feature the link on your wikipeople page, it can be done in the Reference information section. Open the edit tab and the Reference information section. In this section you will see an expandable section "Link to other Web sites". Open it and select website from the drop down. In the box labeled URL, paste the URL for your website. A label can be added as a short description. Then click "Save" at the bottom.
[edit] Tags
Tags are links to other concept entries. Each author entry has the tag "person" but other more specific tags can be added. For instance, the tag for professions such as "biologist" can be added if this accurately describes the person. To edit this section, click on the edit tab, scroll down and expand the tag section. Click on the dropdown meun and a box will appear where you can begin typing. Matches will appear in the drop down and you can scroll through them using the 'previous' and 'next' functions next to the drop down box. When available, the definition of the concepts are shown on the right. Select the correct concept and click 'save' at the bottom of the page. Before clicking 'Save', it is also possible, but not necessary, to write a short note in the 'Summary' box (above the 'Save' button) to briefly indicate the changes you've made to the page.
[edit] Pointers to this person
This table lists other concepts that feature the person in their entries. For example, every publication that you've authored (and has been attributed to you) features you, and should be listed in this section. For each of your concepts of interest, you can visit the concept entry and look at the 'pointers to this concept' section and see people who have an interest in that particular concept. This table cannot be changed but is modified accordingly when other concepts are changed.
[edit] Details on specific sections of concept entries
[edit] Concept entry title
Every concept entry has a title. The title is usually the term that is preferred term for the life sciences. This does not always mean that the title will be scientific jargon; the title and preferred term can also be the common term. For instance, the scientific term for jaguar is Panthera onca but the title of the entry is jaguars. For a newly entered concept, the title will be the first term entered when creating the concept entry.
[edit] Definition
Two concepts may share the same preferred term or title but to be distinguished as separate concepts they must have different definitions.
A single concept may have different definitions depending on your perspective. For instance, the definition for DNA from one perspective is "The molecules inside cells that carry genetic information and pass it from one generation to the next" while another definition specifies "consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine)." If a definition that is already present needs to modified to improve clarity and precision, go ahead and edit. If there is no definition that represents your perspective, simply add a new definition.
[edit] Also known as
On the edit page, in the 'Also known as' section, it is possible to enter synonyms for the concept. There are also 3 other possible features that can be attached to each synonym. These are: synonym scope, preferred in, and reference information. Synonym scope is used to indicate whether a specific synonym is a broad synonym, narrow synonym, exact synonym or related synonym. The 'preferred in' feature indicates the specific context where the synonym is used. For scientific concepts, 'preferred in' will usually specify that the synonym is the preferred term for a specific domain. The 'reference information' is usually used to give evidence for the entered synonym.
The specific synonym must be saved before data for 'synonym scope', 'preferred in' and 'reference information' can be added to these features. To save, scroll down to the bottom of the page and click the 'Save' button. Before clicking 'Save', it is also possible, but not necessary, to write a short note in the 'Summary' box (next to the 'Save' button) to briefly indicate the changes you've made to the entry.
[edit] Functional information
- Free text
To add a free text comment, you must choose a 'Connection' that is appropriate for your comment. On the edit tab, open the Functional information section and then the 'Add free text' subsection. In the 'Add free text' table, the 'Connection' is found in the roll-down menu following the 'Remove' column and before the 'Text' column. The 'Connection' indicates how the free text comment relates to the concept entry. In the functional information section, A 'Connection' must be chosen to accompany the comment or else it will not be saved. After the text is added in the text box, scroll down to the bottom and click 'Save'.
List of Functional information connections for free text comments
has function: General description of the function(s) of a protein
has catalytic activity: Description of the reaction(s) catalyzed by an enzyme
has cofactor: Description of any non-protein substance required by an enzyme for its catalytic activity
enzyme regulation by: Description of an enzyme regulatory mechanism
induced by: Description of the compound(s) or condition(s) that regulate gene expression
interacts with: Conveys information relevant to binary protein-protein interaction
gene product is element in pathway: Description of the metabolic pathway(s) with which a protein is associated
RNA editing causes: Description of any type of RNA editing that leads to one or more amino acid changes
- Link to other concept entries
New functional connections can be added in edit mode in any subsection that says 'Link to other concepts' or in any place that offers a roll-down menu. First, let's look at the 'Link to other concepts'. Clicking the plus/expand sign for the 'Link to other concepts' subsection, opens a table with the columns 'Remove', 'Connection', 'Other concept', 'Reference information', and several columns with the titles of the different contributors (Community, Swiss-Prot, NLM, etc).
To add a connection to another concept entry, you must choose from the first roll-down menu (in the column 'Connection') a suitable connection between the wiki concept you are editing and another wiki entry. In the second roll-down menu, the column labeled 'Other concept', you choose a second wiki concept.
List of Functional information connections for links to other concept entries
gene product has molecular function:
performs: EC number
[edit] Localization and spatial information
has subcellular localization: Description of the subcellular location of the mature protein
gene product expressed in tissue: Description of the tissue-specific expression of mRNA or protein
occurs in: Indicate the species
[edit] Structural and physical information
gene product encoded by gene: On a protein concept entry used to specify the corresponding gene name
gene encodes gene product: On a gene concept entry used to specify the corresponding protein name
has alternative products: Description of the existence of related protein sequence(s) produced by alternative splicing of the same gene, alternative promoter usage, ribosomal frameshifting or by the use of alternative initiation codons
has domain description: Description of the domain structure of a protein
has posttranslational modification: Description of any chemical alternation of a polypeptide (proteolytic cleavage, amino acid modifications including crosslinks).
has polymorphism: Description of polymorphism(s)
gene product has structural domain or motif: Description of the domain(s) or motif(s) (sequence or structural) of a protein with other proteins has mass spectrometry data: Reports the exact molecular weight of a protein or part of a protein as determined by mass spectrometric methods
component of: Description of the quaternary structure of a protein and any kind of interactions with other proteins or protein complexes; except for receptor-ligand interactions, which are described in the topic 'has function'
[edit] Pharmaceutical information
is an allergen: Information relevant to allergenic proteins
is a pharmaceutical: Description of the use of a protein as a pharmaceutical drug
has toxic dose: Description of the lethal dose (LD), paralytic dose (PD) or effective dose of a protein
has biophysicochemical properties: Description of the information relevant to biophysical and physicochemical data and information on pH dependence, temperature dependence, kinetic parameters, redox potentials, and maximal absorption
[edit] Temporal information
has developmental stage expression: Description of the developmentally-specific expression of mRNA or protein
[edit] Conceptual and other information
similarity confers association with: Similaritie(s) (sequence or structural) of a protein with other protein families
gene product malfunction associated with disease: Description of the disease(s) associated with a deficiency of a protein
gene product plays role in biological process:
has miscellaneous information
[edit] Terminological information
The association between pages is given by a relationship indicating a hierarchical connection
[edit] Reference information
source
[edit] Tags
For proteins: Amino Acid, Peptide, or Protein For genes: Gene or Genome
